Anton is a special purpose supercomputer for biomolecular simulation designed and constructed by D. E. Shaw Research (DESRES). PSC's current system is known as Anton 2 and is a successor to the original Anton 1 machine hosted here.
Anton 2, the next-generation Anton supercomputer, is a 128 node system, made available without cost by DESRES for non-commercial research use by US universities and other not-for-profit institutions, and is hosted by PSC with support from the NIH National Institute of General Medical Sciences. It replaced the original Anton 1 system in the fall of 2016.
Anton was designed to dramatically increase the speed of molecular dynamics (MD) simulations compared with the previous state of the art, allowing biomedical researchers to understand the motions and interactions of proteins and other biologically important molecules over much longer time periods than was previously accessible to computational study. The MD research community is using the Anton 2 machine at PSC to investigate important biological phenomena that due to their intrinsically long time scales have been outside the reach of even the most powerful general-purpose scientific computers. Application areas include biomolecular energy transformation, ion channel selectivity and gating, drug interactions with proteins and nucleic acids, protein folding and protein-membrane signaling.
Anton 2 is allocated annually via a Request for Proposal with proposals reviewed by a committee convened by the National Research Council at the National Academies. To qualify for an allocation on Anton 2, the principal investigator must be a faculty or staff member at a U.S. academic or non-profit research institution.
Applications are not currently being accepted. Watch for an announcement of the next application opportunity opening next spring.
A workshop is offered each fall covering all aspects of running MD simulations on Anton 2. It is by invitation only for those who received an allocations award in the most recent opportunity. See more about the workshop.
Anton End User Agreement
All users who are awarded time on Anton2 must complete the Anton End User Agreement (EUA) acknowledging that they have read and understood their responsibilities as an Anton2 user and agree to comply. Once it is signed, return the EUA to firstname.lastname@example.org.
Acknowledgement in publications
Please use the following paragraph (or similiar) to cite your work conducted on Anton. Proper acknowledgment is critical for our ability to solicit continued funding for the project.
Acknowledgement for Anton 2
Anton 2 computer time was provided by the Pittsburgh Supercomputing Center (PSC) through Grant R01GM116961 from the National Institutes of Health. The Anton 2 machine at PSC was generously made available by D.E. Shaw Research.
The proper citation for Anton 2 is:
Shaw, David E., J.P. Grossman, Joseph A. Bank, Brannon Batson, J. Adam Butts, Jack C. Chao, Martin M. Deneroff, et al. “Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer,” 41–53. IEEE, 2014. doi:10.1109/SC.2014.9.
Acknowledgement for Anton 1
Anton computer time was provided by the Pittsburgh Supercomputing Center (PSC) through Grant R01GM116961 from the National Institutes of Health. The Anton machine at PSC was generously made available by D.E. Shaw Research.
The proper citation for the Anton machine is
Millisecond-Scale Molecular Dynamics Simulations on Anton, D. E. Shaw et al., Proceedings of the ACM/IEEE Conference on Supercomputing (SC09), Portland, Oregon (2009).
See project summaries, including trajectory files, for some Anton 1 research.
Here are highlights of just some of the groundbreaking research enabled by Anton:
Molecular mechanisms of cataract formation. Identified the enhanced inter-protein interactions that lead to large-scale aggregation. Wong, Eric K., Vera Prytkova, J. Alfredo Freites, Carter T. Butts, and Douglas J. Tobias. Biochemistry 2019. https://doi.org/10.1021 /acs.
Molecular mechanisms of arrestin activation - Simulations provide a structural foundation for the design of functionally selective ligands that lead to particular GPCR signaling profiles. N. Latorraca and R. Dror. doi:10.1038/s41586-018-0077-3
Uncovering new ways to target flu viruses - A conserved amino acid could provide a target toward a universal vaccine for viruses. Xingcheng Lin, Jeffrey K. Noel, Qinghua Wang, Jianpeng Ma, and Jose Onuchic. doi:10.1073/pnas.1805442115.
Kink formation is required for lateral gating in BamA - Simulations of BamA reveal a dynamic gating between the N- and C-terminal strands at the barrel seam. Using free-energy calculations and mutagenesis experiments, it was determined that the C-terminus has to kink inward for efficient opening. lateral gating in BamA. Karl Lundquist, Jeremy Bakelar, Nicholas Noinaj, and JC Gumbart. doi:10.1073/pnas.1722530115
World’s Tiniest Test Tubes in Alzheimer’s Protein Simulation - Simulations of plaque-forming beta amyloid molecules offer insights towards possible Alzheimer’s drug therapies. From PSC's Science Highlights Fall 2018. G. Eskici and P.H. Axelsen. doi:10.1021/acs.langmuir.7b04192.
"Sticky and Loose Ends” Shed Light on Heart Health - Simulations show APOA1 protein ends link to hold together “the good cholesterol”. From PSC's Science Highlights Fall 2018. Mohsen Pourmousa, Richard Pastor, Jere Segrest, et. al. doi: 10.1073/pnas.1721181115
Locked, Not Loaded - New target in HIV-1 replication. Simulations may lead to more effective anti-maturation drugs to fight AIDS and possibly other viral diseases. From PSC's Science Highlights Spring 2018. J. Perilla et al. doi:10.1038/s41467-017-01856-y.
Inner Space - Work on Anton highlights the importance of empty space for protein function. Simulations of T4 lysozyme L99A show that big gaps opened up in the protein, which “let in” molecules roughly the size of drug molecules. From PSC's Science Highlights Fall 2017.
Hooked Up - Simulations on Anton discover the critical role disulfides play in holding together MCoTI-II, a natural pesticide that would fall apart without disulfide bridges. From PSC's Science Highlights Spring 2017.
“The Dynamics of Single Protein Molecules Is Non-Equilibrium and Self-Similar over Thirteen Decades in Time.” Nature Physics 12, no. 2 (2016): 171–74. doi:10.1038/nphys3553. Hu, Xiaohu, Liang Hong, Micholas Dean Smith, Thomas Neusius, Xiaolin Cheng, and Jeremy C. Smith. This article was highlighted in the cover of Nature Physics and discussed in the following article: Metzler R, News and Views Protein physics: Forever ageing, Nature Phys., 2016, 12, 113–114, doi:10.1038/nphys3585.
"Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide". Biophysical Journal 110, no. 8 (April 2016): 1744–52. doi:10.1016/j.bpj.2016.03.027. Zhang, Yi, Klaus Schulten, Martin Gruebele, Paramjit S. Bansal, David Wilson, and Norelle L. Daly. This article was featured on the cover of the Biophysical Journal.
Island time: “Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin.” Biophysical Journal 109, no. 5 (September 2015): 948–55. doi:10.1016/j.bpj.2015.07.036 Sodt, Alexander J., Richard W. Pastor, and Edward Lyman. This study was featured on the cover of the Biophysical Journal and highlighted as New and Notable: http://www.cell.com/biophysj/abstract/S0006-3495(15)00772-9
A TUG Felt Elsewhere - Anton simulations show how drug-producing enzyme is enhanced by changes far from reactive site, from PSC’s Projects in Scientific Computing, Fall 2014.
Two Steps Forward, One Step Back - molecular dynamics simulations disclose how water leaving and then re-entering the potassium channel delays its return to the active state, from PSC's Projects in Scientific Computing, Spring 2014.
A Movie is Worth a Million Pictures - structural dynamics simulations illuminate the mechanisms of sodium-coupled substrate binding/release in an aspartate transporter, from PSC's 2013 annual report, Projects in Scientific Computing
Epic Microseconds - four projects yielding invaluable insights into the structure and function of proteins from PSC's 2012 annual report, Projects in Scientific Computing
Protein Research Leaps Forward - four projects in MD simulation from PSC's 2011 annual report, Projects in Scientific Computing
Atomic-Level Characterization of the Structural Dynamics of Proteins - This paper, published in Science, details the first millisecond MD simulation on Anton.
Shaw, David E., Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana, Ron O. Dror, Michael P. Eastwood, Joseph A. Bank, John M. Jumper, John K. Salmon, Yibing Shan, Willy Wriggers. "Atomic-Level Characterization of the Structural Dynamics of Proteins" Science 15 Oct 2010: 341-346 DOI: 10.1126/science.1187409
Millisecond-scale molecular dynamics simulations on Anton - This paper (Gordon Bell prize winner for best paper at SC09 ) contains measurements of energy conservation on Anton that you can use to compare with your own simulations.
Publications for research that made use of Anton or Anton 2 at PSC:
Balusek, Curtis, Hyea Hwang, Chun Hon Lau, Karl Lundquist, Anthony Hazel, Anna Pavlova, Diane L. Lynch, Patricia H. Reggio, Yi Wang, and James C. Gumbart. “Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.” Journal of Chemical Theory and Computation, June 20, 2019. https://doi.org/10.1021/acs.jctc.9b00160.
- Biggers, Laurence, Hadeer Elhabashy, Edward Ackad, and Mohammad S. Yousef. “Molecular Dynamics Simulations of an Engineered T4 Lysozyme Exclude Helix to Sheet Transition, and Provide Insights into Long Distance, Intra‐Protein Switchable Motion.” Protein Science, November 8, 2019. https://doi.org/10.1002/pro.3780.
Boiteux, Céline, Emelie Flood, and Toby W. Allen. “Comparison of Permeation Mechanisms in Sodium-Selective Ion Channels.” Neuroscience Letters 700 (May 2019): 3–8. https://doi.org/10.1016/j.neulet.2018.05.036.
Botello-Smith, Wesley M., Wenjuan Jiang, Han Zhang, Alper D. Ozkan, Yi-Chun Lin, Christine N. Pham, Jérôme J. Lacroix, and Yun Luo. “A Mechanism for the Activation of the Mechanosensitive Piezo1 Channel by the Small Molecule Yoda1.” Nature Communications 10, no. 1 (December 2019). https://doi.org/10.1038/s41467-019-12501-1.
Cao, Shufen, Stacey Chung, SoonJeung Kim, Zhenlu Li, Danny Manor, and Matthias Buck. “K-Ras G-Domain Binding with Signaling Lipid Phosphatidyl Inositol (4,5) Phosphate (PIP2): Membrane Association, Protein Orientation and Function.” Journal of Biological Chemistry 294 (February 21, 2019): 7064–84. https://doi.org/10.1074/jbc.RA118.004021.
- Dan, Qingyun, Sean A. Newmister, Kimberly R. Klas, Amy E. Fraley, Timothy J. McAfoos, Amber D. Somoza, James D. Sunderhaus, et al. “Fungal Indole Alkaloid Biogenesis through Evolution of a Bifunctional Reductase/Diels–Alderase.” Nature Chemistry, September 23, 2019. https://doi.org/10.1038/s41557-019-0326-6.
Ellis-Guardiola, Ken, Huan Rui, Ryan L Beckner, Poonam Srivastava, Narayanasami Sukumar, Benoît Roux, and Jared C. Lewis. “Crystal Structure and Conformational Dynamics of Pyrococcus Furiosus Prolyl Oligopeptidase.” Biochemistry 58, no. 12 (February 20, 2019): 1616–1626. https://doi.org/10.1021/acs.biochem.9b00031.
Freites, J. Alfredo, Karin L. Németh-Cahalan, James E. Hall, and Douglas J. Tobias. “Cooperativity and Allostery in Aquaporin 0 Regulation by Ca2+.” Biochimica et Biophysica Acta (BBA) - Biomembranes 1861, no. 5 (May 2019): 988–96. https://doi.org/10.1016/j.bbamem.2019.02.007.
- Ghysels, An, Andreas Krämer, Richard M. Venable, Walter E. Teague, Edward Lyman, Klaus Gawrisch, and Richard W. Pastor. “Permeability of Membranes in the Liquid Ordered and Liquid Disordered Phases.” Nature Communications 10, no. 1 (December 2019). https://doi.org/10.1038/s41467-019-13432-7.
Guros, N. “Advancements in Label-Free Biosensing Using Field-Effect Transistors and Aided by Molecular Dynamics Simulations.” Ph.D. Thesis, University of Maryland, 2019.
- Guros, Nicholas B., Arvind Balijepalli, and Jeffery B. Klauda. “Microsecond-Timescale Simulations Suggest 5-HT–Mediated Preactivation of the 5-HT 3A Serotonin Receptor.” Proceedings of the National Academy of Sciences, December 23, 2019, 201908848. https://doi.org/10.1073/pnas.1908848117.
Hashemi, Mohtadin, Yuliang Zhang, Zhengjian Lv, and Yuri L. Lyubchenko. “Spontaneous Self-Assembly of Amyloid β (1–40) into Dimers.” Nanoscale Advances 1, no. 10 (2019): 3892–99. https://doi.org/10.1039/C9NA00380K.
Huang, Pei-Tzu, Brady James Summers, Chaoyi Xu, Juan R. Perilla, Viacheslav Malikov, Mojgan H. Naghavi, and Yong Xiong. “FEZ1 Is Recruited to a Conserved Cofactor Site on Capsid to Promote HIV-1 Trafficking.” Cell Reports 28, no. 9 (August 2019): 2373-2385.e7. https://doi.org/10.1016/j.celrep.2019.07.079.
Hwang, Wonmuk, and Martin Karplus. “Structural Basis for Power Stroke vs. Brownian Ratchet Mechanisms of Motor Proteins.” Proceedings of the National Academy of Sciences 116, no. 40 (October 1, 2019): 19777–85. https://doi.org/10.1073/pnas.1818589116.
- Immadisetty, Kalyan, Jeevapani Hettige, and Mahmoud Moradi. “Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter.” ACS Central Science 5, no. 1 (n.d.): 43–56. https://doi.org/DOI: 10.1021/acscentsci.8b00480.
Jekhmane, Shehrazade, João Medeiros-Silva, Jing Li, Felix Kümmerer, Christoph Müller-Hermes, Marc Baldus, Benoît Roux, and Markus Weingarth. “Shifts in the Selectivity Filter Dynamics Cause Modal Gating in K+ Channels.” Nature Communications 10, no. 123 (December 2019). https://doi.org/10.1038/s41467-018-07973-6.
Kang, Xue, Christopher Elson, Jackson Penfield, Alex Kirui, Adrian Chen, Liqun Zhang, and Tuo Wang. “Integrated Solid-State NMR and Molecular Dynamics Modeling Determines Membrane Insertion of Human β-Defensin Analog.” Communications Biology 2, no. 1 (December 2019). https://doi.org/10.1038/s42003-019-0653-6.
Lacroix, Jerome. “A Mechanism for the Activation of the Mechanosensitive Piezo1 Channel by the Small Molecule Yoda1.” Nature Communications, n.d.
- Lev, Bogdan, and Toby W. Allen. “Simulating Ion Channel Activation Mechanisms Using Swarms of Trajectories.” Journal of Computational Chemistry, November 19, 2019. https://doi.org/10.1002/jcc.26102.
- Li, Zhen-lu, and Matthias Buck. “Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom Molecular Dynamics Simulations, Confirming a Stepwise Association Process for Native Protein–Protein Interactions.” Journal of Chemical Theory and Computation 15, no. 8 (August 13, 2019): 4318–31. https://doi.org/10.1021/acs.jctc.9b00195.
Liao, Chenyi, Victor May, and Jianing Li. “Assessment of Conformational State Transitions of Class B GPCRs Using Molecular Dynamics.” In G Protein-Coupled Receptor Signaling, edited by Mario Tiberi, 1947:3–19. New York, NY: Springer New York, 2019. https://doi.org/10.1007/978-1-4939-9121-1_1.
Lundquist, Karl P., and James C. Gumbart. “Presence of Substrate Aids Lateral Gate Separation in LptD.” Biochimica et Biophysica Acta (BBA) - Biomembranes, July 2019, 183025. https://doi.org/10.1016/j.bbamem.2019.07.013.
Lv, Zhengjian, Mohtadin Hashemi, Siddhartha Banerjee, Karen Zagorski, Jean-Christophe Rochet, and Yuri L. Lyubchenko. “Assembly of α-Synuclein Aggregates on Phospholipid Bilayers.” Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1867, no. 9 (September 2019): 802–12. https://doi.org/10.1016/j.bbapap.2019.06.006.
Majumdar, Bibhab Bandhu, Vera Prytkova, Eric K. Wong, J. Alfredo Freites, Douglas J. Tobias, and Matthias Heyden. “Role of Conformational Flexibility in Monte Carlo Simulations of Many-Protein Systems.” Journal of Chemical Theory and Computation 15, no. 2 (February 12, 2019): 1399–1408. https://doi.org/10.1021/acs.jctc.8b00894.
Martynowycz, Michael W., Amy Rice, Konstantin Andreev, Thatyane M. Nobre, Ivan Kuzmenko, Jeff Wereszczynski, and David Gidalevitz. “Salmonella Membrane Structural Remodeling Increases Resistance to Antimicrobial Peptide LL-37.” ACS Infectious Diseases, May 24, 2019. https://doi.org/10.1021/acsinfecdis.9b00066.
McGraw, Claire, Lewen Yang, Ilya Levental, Edward Lyman, and Anne Skaja Robinson. “Membrane Cholesterol Depletion Reduces Downstream Signaling Activity of the Adenosine A2A Receptor.” Biochimica et Biophysica Acta (BBA) - Biomembranes 1861, no. 4 (April 2019): 760–67. https://doi.org/10.1016/j.bbamem.2019.01.001.
Mihailescu, Mihaela, Mirco Sorci, Jolita Seckute, Vitalii I. Silin, Janet Hammer, B. Scott Perrin, Jorge I. Hernandez, et al. “Structure and Function in Antimicrobial Piscidins: Histidine Position, Directionality of Membrane Insertion, and PH-Dependent Permeabilization.” Journal of the American Chemical Society 141, no. 25 (June 26, 2019): 9837–53. https://doi.org/10.1021/jacs.9b00440.
Mohammadi, M. “Computational Studies of Protein-Inhibitor Interactions.” Ph.D., Chemical Engineering, New Hampshire, 2019.
Monje-Galvan, Viviana, Linnea Warburton, and Jeffery B. Klauda. “Setting Up All-Atom Molecular Dynamics Simulations to Study the Interactions of Peripheral Membrane Proteins with Model Lipid Bilayers.” In Intracellular Lipid Transport, edited by Guillaume Drin, 1949:325–39. New York, NY: Springer New York, 2019. https://doi.org/10.1007/978-1-4939-9136-5_22.
- Nangia, Shivangi, Kevin J. Boyd, and Eric R. May. “Molecular Dynamics Study of Membrane Permeabilization by Wild-Type and Mutant Lytic Peptides from the Non-Enveloped Flock House Virus.” Biochimica et Biophysica Acta (BBA) - Biomembranes, October 2019, 183102. https://doi.org/10.1016/j.bbamem.2019.183102.
- Nawrocki, Grzegorz, Wonpil Im, Yugi Sugita, and Michael Feig. “Clustering and Dynamics of Crowded Proteins near Membranes and Their Influence on Membrane Bending.” Proceedings of the National Academy of Sciences, 116 (49): 24562–67. https://doi.org/10.
Nguyen, Phuong T., Kevin R. DeMarco, Igor Vorobyov, Colleen E. Clancy, and Vladimir Yarov-Yarovoy. “Structural Basis for Antiarrhythmic Drug Interactions with the Human Cardiac Sodium Channel.” Proceedings of the National Academy of Sciences 116, no. 8 (February 19, 2019): 2945–54. https://doi.org/10.1073/pnas.1817446116.
Park, Sang-Jun, Jumin Lee, Yifei Qi, Nathan R Kern, Hui Sun Lee, Sunhwan Jo, InSuk Joung, Keehyung Joo, Jooyoung Lee, and Wonpil Im. “CHARMM-GUI Glycan Modeler for Modeling and Simulation of Carbohydrates and Glycoconjugates.” Glycobiology 29, no. 4 (April 1, 2019): 320–31. https://doi.org/10.1093/glycob/cwz003.
Park, Soohyung, and Wonpil Im. “Analysis of Lipid Order States and Domains in Lipid Bilayer Simulations.” Journal of Chemical Theory and Computation 15, no. 1 (January 8, 2019): 688–97. https://doi.org/10.1021/acs.jctc.8b00828.
Perissinotti, Laura, Jiqing Guo, Meruyert Kudaibergenova, James Lees-Miller, Marina Ol’khovich, Angelica Sharapova, German L. Perlovich, et al. “The Pore-Lipid Interface: Role of Amino-Acid Determinants of Lipophilic Access by Ivabradine to the HERG1 Pore Domain.” Molecular Pharmacology 96, no. 2 (August 2019): 259–71. https://doi.org/10.1124/mol.118.115642.
Pinkwart, Kerstin, Falk Schneider, Martyna Lukoseviciute, Tatjana Sauka-Spengler, Edward Lyman, Christian Eggeling, and Erdinc Sezgin. “Nanoscale Dynamics of Cholesterol in the Cell Membrane.” Journal of Biological Chemistry 294, no. 34 (August 23, 2019): 12599–609. https://doi.org/10.1074/jbc.RA119.009683.
Prakash, Priyanka, and Alemayehu A. Gorfe. “Probing the Conformational and Energy Landscapes of KRAS Membrane Orientation.” The Journal of Physical Chemistry B, September 25, 2019. https://doi.org/10.1021/acs.jpcb.9b05796.
Prakash, Priyanka, Douglas Litwin, Hong Liang, Suparna Sarkar-Banerjee, Drew Dolino, Yong Zhou, John F. Hancock, Vasanthi Jayaraman, and Alemayehu A. Gorfe. “Dynamics of Membrane-Bound G12V-KRAS from Simulations and Single-Molecule FRET in Native Nanodiscs.” Biophysical Journal 116, no. 2 (January 2019): 179–83. https://doi.org/10.1016/j.bpj.2018.12.011.
Prigozhin, Maxim B., Yi Zhang, Klaus Schulten, Martin Gruebele, and Taras V. Pogorelov. “Fast Pressure-Jump All-Atom Simulations and Experiments Reveal Site-Specific Protein Dehydration-Folding Dynamics.” Proceedings of the National Academy of Sciences 116, no. 12 (March 19, 2019): 5356–61. https://doi.org/10.1073/pnas.1814927116.
Rajagopal, Nandhini, Flaviyan Jerome Irudayanathan, and Shikha Nangia. “Palmitoylation of Claudin-5 Proteins Influences Their Lipid Domain Affinity and Tight Junction Assembly at the Blood–Brain Barrier Interface.” The Journal of Physical Chemistry B 123, no. 5 (January 28, 2019): 983–93. https://doi.org/10.1021/acs.jpcb.8b09535.
Rice, Amy. “Toward a Comprehensive Atomistic View of Bacterial Outer Membrane Remodeling and Antimicrobial Peptide Susceptibility.” Ph.D., Physics, Illinois Institute of Technology, 2019.
- Rickard, Meredith M., Yi Zhang, Martin Gruebele, and Taras V. Pogorelov. “In-Cell Protein–Protein Contacts: Transient Interactions in the Crowd.” The Journal of Physical Chemistry Letters 10, no. 18 (September 19, 2019): 5667–73. https://doi.org/10.1021/acs.jpclett.9b01556.
- Shahul Hameed, Umar F, Chenyi Liao, Anand K Radhakrishnan, Franceline Huser, Safia S Aljedani, Xiaochuan Zhao, Afaque A Momin, et al. “H-NS Uses an Autoinhibitory Conformational Switch for Environment-Controlled Gene Silencing.” Nucleic Acids Research 47, no. 5 (March 18, 2019): 2666–80. https://doi.org/10.1093/nar/gky1299.
Smaga, Sarah Sierra, Chaoyi Xu, Brady James Summers, Katherine Marie Digianantonio, Juan Roberto Perilla, and Yong Xiong. “MxB Restricts HIV-1 by Targeting the Tri-Hexamer Interface of the Viral Capsid.” Structure, 2019, in press. https://doi.org/10.1101/444067.
Taylor, Bryn C., Christopher T. Lee, and Rommie E. Amaro. “Structural Basis for Ligand Modulation of the CCR2 Conformational Landscape.” Proceedings of the National Academy of Sciences116, no. 17 (April 23, 2019): 8131–36. https://doi.org/10.1073/pnas.1814131116.
Walker, Alice R., Baddam, Nikhil, and Cisneros, G. Andres. “Unfolding Pathways of Hen Egg White Lysozyme in Ethanol.” J. Physical Chemistry B 123, no. 15 (2019): 3267–71. https://doi.org/DOI: 10.1021/acs.jpcb.9b01694.
- Wang, Eric, and Jeffery B. Klauda. “Molecular Structure of the Long Periodicity Phase in the Stratum Corneum.” Journal of the American Chemical Society, October 11, 2019. https://doi.org/10.1021/jacs.9b08995.
Weiner, Michael D., and Gerald W. Feigenson. “Molecular Dynamics Simulations Reveal Leaflet Coupling in Compositionally Asymmetric Phase-Separated Lipid Membranes.” The Journal of Physical Chemistry B 123, no. 18 (May 9, 2019): 3968–75. https://doi.org/10.1021/acs.jpcb.9b03488.
Wildermuth, Kyle D., Viviana Monje-Galvan, Linnea M. Warburton, and Jeffery B. Klauda. “Effect of Membrane Lipid Packing on Stable Binding of the ALPS Peptide.” Journal of Chemical Theory and Computation 15, no. 2 (February 12, 2019): 1418–29. https://doi.org/10.1021/acs.jctc.8b00945.
Winogradoff, David, and Aleksei Aksimentiev. “Molecular Mechanism of Spontaneous Nucleosome Unraveling.” Journal of Molecular Biology 431, no. 2 (January 2019): 323–35. https://doi.org/10.1016/j.jmb.2018.11.013.
Wong, Eric K., Vera Prytkova, J. Alfredo Freites, Carter T. Butts, and Douglas J. Tobias. “Molecular Mechanism of Aggregation of the Cataract-Related ΓD-Crystallin W42R Variant from Multiscale Atomistic Simulations.” Biochemistry, August 8, 2019. https://doi.org/10.1021/acs.biochem.9b00208.
Yang, Lewen, and Edward Lyman. “Local Enrichment of Unsaturated Chains around the A 2A Adenosine Receptor.” Biochemistry, September 19, 2019. https://doi.org/10.1021/acs.biochem.9b00607.
- Yang, Ling, Xiaoting Sun, Ying Ye, Yongtian Lu, Ji Zuo, Wen Liu, Adrian Elcock, and Shun Zhu. “P38α Mitogen-Activated Protein Kinase Is a Druggable Target in Pancreatic Adenocarcinoma.” Frontiers in Oncology 9 (November 26, 2019). https://doi.org/10.3389/fonc.2019.01294.
- Chakraborty, Kaushik, Myungshim Kang, and Sharon M. Loverde. “Molecular Mechanism for the Role of the H2A and H2B Histone Tails in Nucleosome Repositioning.” The Journal of Physical Chemistry B 122, no. 50 (December 20, 2018): 11827–40. https://doi.org/10.1021/acs.jpcb.8b07881.
- Cheng, Mary Hongying, Cihan Kaya, and Ivet Bahar. “Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter.” The Journal of Physical Chemistry B, December 26, 2017. doi: 10.1021/acs.jpcb.7b10340.
- Debiec, Karl T., Matthew J. Whitley, Leonardus M.I. Koharudin, Lillian T. Chong, and Angela M. Gronenborn. “Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.” Biophysical Journal 114, no. 4 (February 2018): 839–55. doi: 10.1016/j.bpj.2018.01.001.
- DeMarco, Kevin R., Slava Bekker, Colleen E. Clancy, Sergei Y. Noskov, and Igor Vorobyov. “Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker D-Sotalol with All-Atom Simulations.” Frontiers in Pharmacology 9 (February 1, 2018). doi: 10.3389/fphar.2018.00026.
- Dick, Robert A., Kaneil K. Zadrozny, Chaoyi Xu, Florian K. M. Schur, Terri D. Lyddon, Clifton L. Ricana, Jonathan M. Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature, August 1, 2018. doi: 10.1038/s41586-018-0396-4
- Eskici, Gozde, and Paul H. Axelsen. “Mass Exchange and Equilibration Processes in AOT Reverse Micelles.” Langmuir 34, no. 7 (February 20, 2018): 2522–30. doi: 10.1021/acs.langmuir.7b04192.
- Flood, Emelie, Céline Boiteux, and Toby W. Allen. “Selective Ion Permeation Involves Complexation with Carboxylates and Lysine in a Model Human Sodium Channel.” Edited by Alexander MacKerell. PLOS Computational Biology 14, no. 9 (September 12, 2018): e1006398. doi: 10.1371/journal.pcbi.1006398
- Gołaś, Ewa I., Magdalena Mozolewska, Pawel Krupa, Cezary Czaplewski, Adam Scheraga, and Adam Liwo. “Use of Coarse-Grained and All-Atom Molecular Dynamics to Study Hsp70 and Hsp40 Chaperone Action.” In Frontiers in Structural Biology, 1:23–46, 2018.
- Gumbart, James C., Martin B. Ulmschneider, Anthony Hazel, Stephen H. White, and Jakob P. Ulmschneider. “Computed Free Energies of Peptide Insertion into Bilayers Are Independent of Computational Method.” The Journal of Membrane Biology, March 8, 2018. doi: 10.1007/s00232-018-0026-y.
- Heppner, David E., Christopher M. Dustin, Chenyi Liao, Milena Hristova, Carmen Veith, Andrew C. Little, Bethany A. Ahlers, et al. “Direct Cysteine Sulfenylation Drives Activation of the Src Kinase.” Nature Communications 9, no. 1 (December 2018). https://doi.org/10.1038/s41467-018-06790-1.
- Hoogerheide, David P., Sergei Yu. Noskov, Adam J. Kuszak, Susan K. Buchanan, Tatiana K. Rostovtseva, and Hirsh Nanda. “Structure of Voltage-Dependent Anion Channel-Tethered Bilayer Lipid Membranes Determined Using Neutron Reflectivity.” Acta Crystallographica Section D Structural Biology 74, no. 12 (December 1, 2018): 1219–32. https://doi.org/10.1107/S2059798318011749
- Islam, Rafique M., Mohsen Pourmousa, Denis Sviridov, Scott M. Gordon, Edward B. Neufeld, Lita A. Freeman, B. Scott Perrin, Richard W. Pastor, and Alan T. Remaley. “Structural Properties of Apolipoprotein A-I Mimetic Peptides That Promote ABCA1-Dependent Cholesterol Efflux.” Scientific Reports 8, no. 1 (December 2018). doi: 10.1038/s41598-018-20965-2.
- Iyer, Sahithya S., Madhusmita Tripathy, and Anand Srivastava. “Fluid Phase Coexistence in Biological Membrane: Insights from Local Nonaffine Deformation of Lipids.” Biophysical Journal 115, no. 1 (July 2018): 117–28. doi: 10.1016/j.bpj.2018.05.021
- Kimanius, D., E. Lindahl, and M. Andersson. “Uptake Dynamics in the Lactose Permease (LacY) Membrane Protein Transporter.” Scientific Reports 8, no. 1 (December 2018). https://doi.org/10.1038/s41598-018-32624-7.
- Latorraca, Naomi R., Jason K. Wang, Brian Bauer, Raphael J. L. Townshend, Scott A. Hollingsworth, Julia E. Olivieri, H. Eric Xu, Martha E. Sommer, and Ron O. Dror. “Molecular Mechanism of GPCR-Mediated Arrestin Activation.” Nature 557, no. 7705 (May 2018): 452–56. doi: 10.1038/s41586-018-0077-3.
- Lee, Byoung-Cheol, George Khelashvili, Maria Falzone, Anant K. Menon, Harel Weinstein, and Alessio Accardi. “Gating Mechanism of the Extracellular Entry to the Lipid Pathway in a TMEM16 Scramblase.” Nature Communications 9, no. 1 (December 2018). doi: 10.1038/s41467-018-05724-1.
- Lee, Hui Sun, Yeonock Oh, Mahn-Joo Kim, and Wonpil Im. “Molecular Basis of Aqueous-like Activity of Lipase Treated with Glucose-Headed Surfactant in Organic Solvent.” The Journal of Physical Chemistry B 122, no. 47 (November 29, 2018): 10659–68. https://doi.org/10.1021/acs.jpcb.8b07686.
- Li, Zhen-Lu, Priyanka Prakash, and Matthias Buck. “A ‘Tug of War’ Maintains a Dynamic Protein–Membrane Complex: Molecular Dynamics Simulations of C-Raf RBD-CRD Bound to K-Ras4B at an Anionic Membrane.” ACS Central Science 4, no. 2 (February 28, 2018): 298–305. doi: 10.1021/acscentsci.7b00593.
- Lin, Xingcheng, Jeffrey K. Noel, Qinghua Wang, Jianpeng Ma, and José N. Onuchic. “Atomistic Simulations Indicate the Functional Loop-to-Coiled-Coil Transition in Influenza Hemagglutinin Is Not Downhill.” Proceedings of the National Academy of Sciences 115, no. 34 (August 21, 2018): E7905–13. doi: 10.1073/pnas.1805442115.
- Liu, Fangming, Hannah Hoag, Chun Wu, Haizhou Liu, Hua Yin, Jianjun Dong, Zhonghua Qian, Feng Miao, Ming Liu, and Jinlai Miao. “Experimental and Simulation Identification of Xanthohumol as an Inhibitor and Substrate of ABCB1.” Applied Sciences 8, no. 5 (April 27, 2018): 681. doi: 10.3390/app8050681.
- Lundquist, Karl, Jeremy Bakelar, Nicholas Noinaj, and James C. Gumbart. “C-Terminal Kink Formation Is Required for Lateral Gating in BamA.” Proceedings of the National Academy of Sciences, August 7, 2018, 201722530. doi: 10.1073/pnas.1722530115.
- Marino, Kristen A., and Marta Filizola. “Investigating Small-Molecule Ligand Binding to G Protein- Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.” In Computational Methods for GPCR Drug Discovery, edited by Alexander Heifetz, 1705:351–64. New York, NY: Springer New York, 2018. doi: 10.1007/978-1-4939-7465-8_17.
- Min, Duyoung, Robert E. Jefferson, Yifei Qi, Jing Yang Wang, Mark A. Arbing, Wonpil Im, and James U. Bowie. “Unfolding of a ClC Chloride Transporter Retains Memory of Its Evolutionary History.” Nature Chemical Biology 14, no. 5 (May 2018): 489–96. doi: 10.1038/s41589-018-0025-4.
- Monje-Galvan, Viviana, and Jeffery B. Klauda. “Preferred Binding Mechanism of Osh4’s ALPS Motif, Insights From Molecular Dynamics.” The Journal of Physical Chemistry B, October 3, 2018. doi: 10.1021/
- Montgomery, David, Alexandra Campbell, Holli-Joi Sullivan, and Chun Wu. “Molecular Dynamics Simulation of Biased Agonists at the Dopamine D2 Receptor Suggests the Mechanism of Receptor Functional Selectivity.” Journal of Biomolecular Structure and Dynamics, August 19, 2018, 1–49. doi: 10.1080/07391102.2018.1513378.
- Newmister, Sean A., Shasha Li, Marc Garcia-Borràs, Jacob N. Sanders, Song Yang, Andrew N. Lowell, Fengan Yu, et al. “Structural Basis of the Cope Rearrangement and Cyclization in Hapalindole Biogenesis.” Nature Chemical Biology, March 12, 2018. doi: 10.1038/s41589-018-0003-x.
- Ohmann, Alexander, Chen-Yu Li, Christopher Maffeo, Kareem Al Nahas, Kevin N. Baumann, Kerstin Göpfrich, Jejoong Yoo, Ulrich F. Keyser, and Aleksei Aksimentiev. “A Synthetic Enzyme Built from DNA Flips 107 Lipids per Second in Biological Membranes.” Nature Communications 9, no. 1 (December 2018). https://doi.org/10.1038/s41467-018-04821-5.
- Palermo, Giulia, Janice S. Chen, Clarisse G. Ricci, Ivan Rivalta, Martin Jinek, Victor S. Batista, Jennifer A. Doudna, and J. Andrew McCammon. “Key Role of the REC Lobe during CRISPR–Cas9 Activation by ‘Sensing’, ‘Regulating’, and ‘Locking’ the Catalytic HNH Domain.” Quarterly Reviews of Biophysics 51 (2018). https://doi.org/10.1017/S0033583518000070.
- Pino-Angeles, Almudena, and Themis Lazaridis. “Effects of Peptide Charge, Orientation, and Concentration on Melittin Transmembrane Pores.” Biophysical Journal 114, no. 12 (June 2018): 2865–74. doi: 10.1016/j.bpj.2018.05.006
- Pourmousa, Mohsen, and Richard W. Pastor. “Molecular Dynamics Simulations of Lipid Nanodiscs.” Biochimica et Biophysica Acta (BBA) - Biomembranes, May 2018. doi: 10.1016/j.bbamem.2018.04.015.
- Pourmousa, Mohsen, Hyun D. Song, Yi He, Jay W. Heinecke, Jere P. Segrest, and Richard W. Pastor. “Tertiary Structure of Apolipoprotein A-I in Nascent High-Density Lipoproteins.” Proceedings of the National Academy of Sciences 115, no. 20 (May 15, 2018): 5163–68. doi: 10.1073/pnas.1721181115.
- Prakash, Priyanka, Douglas Litwin, Hong Liang, Suparna Sarkar-Banerjee, Drew Dolino, Yong Zhou, John F. Hancock, Vasanthi Jayaraman, and Alemayehu A. Gorfe. “Dynamics of Membrane-Bound G12V KRAS Investigated by Simulation and Single Molecule FRET in Native Nanodiscs.” Biophysical Journal, December 2018. https://doi.org/10.1016/j.bpj.2018.12.011.
- Prévost, Coline, Morris E. Sharp, Nora Kory, Qingqing Lin, Gregory A. Voth, Robert V. Farese, and Tobias C. Walther. “Mechanism and Determinants of Amphipathic Helix-Containing Protein Targeting to Lipid Droplets.” Developmental Cell 44, no. 1 (January 2018): 73-86.e4. https://doi.org/10.1016/j.devcel.2017.12.011.
- Rice, Amy, and Jeff Wereszczynski. “Atomistic Scale Effects of Lipopolysaccharide Modifications on Bacterial Outer Membrane Defenses.” Biophysical Journal 114, no. 6 (March 2018): 1389–99. doi: 10.1016/j.bpj.2018.02.006
- Sader, Safaa, Kumar Anant, and Chun Wu. “To Probe Interaction of Morphine and IBNtxA with 7TM and 6TM Variants of the Human μ-Opioid Receptor Using All-Atom Molecular Dynamics Simulations with an Explicit Membrane.” Physical Chemistry Chemical Physics 20, no. 3 (2018): 1724–41. doi: 10.1039/C7CP06745C.
- Shahul Hameed, Umar F, Chenyi Liao, Anand K Radhakrishnan, Franceline Huser, Safia S Aljedani, Xiaochuan Zhao, Afaque A Momin, et al. “H-NS Uses an Autoinhibitory Conformational Switch for Environment-Controlled Gene Silencing.” Nucleic Acids Research, December 28, 2018. https://doi.org/10.1093/nar/gky1299.
- Sparks, Samuel, Deniz B. Temel, Michael P. Rout, and David Cowburn. “Deciphering the ‘Fuzzy’ Interaction of FG Nucleoporins and Transport Factors Using Small-Angle Neutron Scattering.” Structure 26, no. 3 (March 2018): 477–484.e4. doi: 10.1016/j.str.2018.01.010.
- Tran, Kelly. “Reduction Potential Properties of Electron Transfer Proteins.” Georgetown University, Ph.D. Thesis, 2018.
- Weiner, Michael D. “Coupling and Clustering in Molecular Dynamics Simulations of Lipid Membrane Biophysics.” Cornell Univ., 2018.
- Wong, Eric K. “Modeling the Structure and Dynamics of Gamma-Crystallins and Their Cataract-Related Variants,” 2018. Ph.D. Thesis, Univ. of California, Irvine.
- Yu, Alvin, and Albert Y. Lau. “Glutamate and Glycine Binding to the NMDA Receptor.” Structure, June 2018. doi: 10.1016/j.str.2018.05.004.
- Yu, Alvin, Héctor Salazar, Andrew J.R. Plested, and Albert Y. Lau. “Neurotransmitter Funneling Optimizes Glutamate Receptor Kinetics.” Neuron 97, no. 1 (January 2018): 139–149.e4. doi: 10.1016/j.neuron.2017.11.024.
- Ahuja, Lalima G., Alexandr P. Kornev, Christopher L. McClendon, Gianluigi Veglia, and Susan S. Taylor. “Mutation of a Kinase Allosteric Node Uncouples Dynamics Linked to Phosphotransfer.” Proceedings of the National Academy of Sciences 114, no. 6 (February 7, 2017): E931–40. doi: 10.1073/pnas.1620667114.
- Bargiello, Thaddeus A., Seunghoon Oh, Qingxiu Tang, Nicholas K. Bargiello, Terry L. Dowd, and Taekyung Kwon. “Gating of Connexin Channels by Transjunctional-Voltage: Conformations and Models of Open and Closed States.” Biochimica et Biophysica Acta (BBA) - Biomembranes, May 2017. doi: 10.1016/j.bbamem.2017.04.028.
- Beaven, Andrew H., Andreia M. Maer, Alexander J. Sodt, Huan Rui, Richard W. Pastor, Olaf S. Andersen, and Wonpil Im. “Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation.” Biophysical Journal 112, no. 6 (March 2017): 1185–97. doi: 10.1016/j.bpj.2017.01.028.
- Cheng, Mary Hongying, Jennie Garcia-Olivares, Steven Wasserman, Jennifer DiPietro, and Ivet Bahar. “Allosteric Modulation of Human Dopamine Transporter Activity under Conditions Promoting Its Dimerization.” Journal of Biological Chemistry 292, no. 30 (July 28, 2017): 12471–82. doi: 10.1074/jbc.M116.763565.
- Debiec, Karl T. “Integration of NMR and SAXS with Atomistic Simulations for Characterizing the Structure and Dynamics of Multi-Domain Proteins.” 2017 Univ. of Pittsburgh Ph.D. Thesis.
- Elnatan, D., M. Betegon, Y. Liu, T. Ramelot, M.A. Kennedy, and D. Agard. “Symmetry Broken and Rebroken during the ATP Hydrolysis Cycle of the Mitochondrial Hsp90 TRAP1.” eLife 2017 6:e25235, 2017, 107094. doi: DOI:10.7554/eLife.25235.
- Eskici, Gözde, and Paul H Axelsen. “Amyloid Beta Peptide Folding in Reverse Micelles.” Journal of the American Chemical Society 139, no. 28 (July 19, 2017): 9566–75. doi: 10.1021 /jacs.7b03333.
- Gaieb, Zied, and Dimitrios Morikis. “Conformational Heterogeneity in CCR7 Undergoes Transitions to Specific States upon Ligand Binding.” Journal of Molecular Graphics and Modelling 74 (June 2017): 352–58. doi: 10.1016/j.jmgm.2017.04.012.
- Gaieb, Zied, and Dimitrios Morikis. “Detection of Side Chain Rearrangements Mediating the Motions of Transmembr ane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors.” Computational and Structural Biotechnology Journal 15 (2017): 131–37. doi:10.1016/j.csbj.2017.01.001.
- Ghaemi, Zhaleh, Irisbel Guzman, David Gnutt, Zaida Luthey-Schulten, and Martin Gruebele. “Role of Electrostatics in Protein-RNA Binding: The Global vs . the Local Energy Landscape.” The Journal of Physical Chemistry B, August 14, 2017. doi: 10.1021/acs.jpcb.7b04318.
- Guan, Zhuo, Maria Bykhovskaia, Ramon A Jorquera, Roger Bryan Sutton, Yulia Akbergenova, and J Troy Littleton. “A Synaptotagmin Suppressor Screen Indicates SNARE Binding Controls the Timing and Ca2+ Cooperativity of Vesicle Fusion.” eLife 6 (September 12, 2017). https://doi.org /10.7554/eLife.28409.
- Hoogerheide, David P., Sergei Y. Noskov, Daniel Jacobs, Lucie Bergdoll, Vitalii Silin, David L. Worcester, Jeff Abramson, Hirsh Nanda, Tatiana K. Rostovtseva, and Sergey M. Bezrukov. “Structural Features and Lipid Binding Domain of Tubulin on Biomimetic Mitochondrial Membranes.” Proceedings of the National Academy of Sciences 114, no. 18 (May 2, 2017): E3622–31. doi: 10.1073/pnas.1619806114.
- Huang, Yu-ming Mindy, Mark Anthony V. Raymundo, Wei Chen, and Chia-en A. Chang. “Mechanism of the Association P athways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease.” Biochemistry, January 6, 2017. doi:10.1021/acs.biochem.6b01112.
- Hwang, Wonmuk, Matthew Lang, and Martin Karplus. “Kinesin Motility Driven by Subdomain Dynamics.” eLife 6 (November 7, 2017). doi: 10.7554/eLife.28948.
- Lee, Hui Sun, and Wonpil Im. “Effects of N-Glycan Composition on Structure and Dynamics of IgG1Fc and Their Implications for Antibody Engineering.” Scientific Reports 7, no. 1 (December 2017). doi: 10.1038/s41598-017-12830-5.
- Lee, Hui Sun, and Wonpil Im. “Transmembrane Motions of PglB Induced by LLO Are Coupled with EL5 Loop Conformational Changes Necessary for OST Activity.” Glycobiology 27, no. 8 (August 2017): 734–42. doi: 10.1093/glycob/cwx052.
- Li, Jing, Jared Ostmeyer, Eliot Boulanger, Huan Rui, Eduardo Perozo, and Benoît Roux. “Chemical Substitutions in the Selectivity Filter of Potassium Channels Do Not Rule out Constricted-like Conformations for C-Type Inactivation.” Proceedings of the National Academy of Sciences, October 2, 2017, 201706983. doi: 10.1073/pnas.1706983114.
Liao, Chenyi, Xiaochuan Zhao, Matthias Brewer, Victor May, and Jianing Li. “Conformational Transitions of the Pituitary Adenylate Cyclase-Activating Polypeptide Receptor, a Human Class B GPCR.” Scientific Reports 7, no. 1 (December 2017). doi: 10.
- Lipkin, Richard. “Computational Investigation of the Pore Formation Mechanism of Beta-Hairpin Antimicrobial Peptides" (2017). CUNY Academic Works.” City University of New York, 2017. http://academicworks.cuny.edu/gc_etds/2380.
- Lipkin, Richard, Almudena Pino-Angeles, and Themis Lazaridis. “Transmembrane Pore Structures of β-Hairpin Antimicrobial Peptides by All-Atom Simulations.” The Journal of Physical Chemistry B, September 7, 2017. doi: 10.1021/acs.jpcb.7b06591.
- Liu, Hanzhong, Qingzhe Tan, Li Han, and Shuanghong Huo. “Observations on AMBER Force Field Performance under the Conditions of Low pH and High Salt Concentrations.” The Journal of Physical Chemistry B, September 29, 2017. doi: 10.1021/acs.jpcb.7b07528.
- Maffeo, Christopher, and Aleksei Aksimentiev. “Molecular Mechanism of DNA Association with Single-Stranded DNA Binding Protein.” Nucleic Acids Research 45, no. 21 (December 1, 2017): 12125–39. doi: 10.1093/nar/gkx917.
Mohammadiarani, Hossein. “Simulation Studies of Signaling and Regulatory Proteins.” Ph.D., Univ. of New Hampshire, 2017. https://search.proquest.com/docview/2013309155?pq-origsite=gscholar.
- Monje-Galvan, Viviana. “Computational Studies of Membrane Models and their Interaction with a Peripheral Protein in Yeast, and Disruption of the Water-Oil Interface by a Hydrotrope.” Ph.D., University of Maryland, College Park, 2017.
- Pohorille, Andrew, Michael A. Wilson, and Gareth Shannon. “Flexible Proteins at the Origin of Life.” Life 7, no. 2 (June 5, 2017): 23. doi: 10.3390/life7020023.
- Rouviere, Eric, Clément Arnarez, Lewen Yang, and Edward Lyman. “Identification of Two New Cholesterol Interaction Sites on the A2A Adenosine Receptor.” Biophysical Journal 113, no. 11 (December 2017): 2415–24. https://doi.org/10.1016/j.bpj.2017.09.027.
- Seyler, Sean. “Computational Approaches to Simulation and Analysis of Large Conformational Transitions in Proteins.” Arizona Sate University, Ph.D. Thesis.
- Shengjuler, Djoshkun, Yan Mei Chan, Simou Sun, Ibrahim M. Moustafa, Zhen-Lu Li, David W. Gohara, Matthias Buck, Paul S. Cremer, David D. Boehr, and Craig E. Cameron. “The RNA-Binding Site of Poliovirus 3C Protein Doubles as a Phosphoinositide-Binding Domain.” Structure 25, no. 12 (December 2017): 1875–1886.e7. doi: 10.1016/j.str.2017.11.001.
- Venable, Richard M., Helgi I. Ingólfsson, Michael G. Lerner, B. Scott Perrin, Brian A. Camley, Siewert J. Marrink, Frank L. H. Brown, and Richard W. Pastor. “Lipid and Peptide Diffusion in Bilayers: The Saffman–Delbrück Model and Periodic Boundary Conditions.” The Journal of Physical Chemistry B, January 6, 2017. doi: 10.1021/acs.jpcb.6b09111.
- Wang, Mingzhang, Caitlin M. Quinn, Juan R. Perilla, Huilan Zhang, Randall Shirra, Guangjin Hou, In-Ja Byeon, et al. “Quenching Protein Dynamics Interferes with HIV Capsid Maturation.” Nature Communications 8, no. 1 (December 2017). doi: 10.1038/s41467-017-01856-y.
- Wei, Chenyu, and Andrew Pohorille. “Sequence-Dependent Interfacial Adsorption and Permeation of Dipeptides across Phospholipid Membranes.” The Journal of Physical Chemistry B, October 5, 2017. doi: 10.1021/acs.jpcb.7b08238.
- Wood, Mona L., J. Alfredo Freites, Francesco Tombola, and Douglas J. Tobias. “Atomistic Modeling of Ion Conduct ion Through the Voltage-Sensing Domain of the Shaker K + Ion Channel.” The Journal of Physical Chemistry B, January 11, 2017. doi: 10.1021/acs.jpcb.6b12639.
- Yelshanskaya, Maria V., Samaneh Mesbahi-Vasey, Maria G. Kurnikova, and Alexander I. Sobolevsky. “Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating.” Scientific Reports 7, no. 1 (April 21, 2017): 1050. https://doi.org/10.1038/s41598-017-01146-z.
- Yonkunas, Michael, Maiti Buddhadev, Jose C. Flores Canales, and Maria G. Kurnikova. “Configurational Preference of the Glutamate Receptor Ligand Binding Domain Dimers.” Biophysical Journal 112, no. 11 (June 2017): 2291–2300. doi: 10.1016/j.bpj.2017.04.042.
- Yu, Alvin. “Computational Investigations of Ionotropic Glutamate Receptor Ligand Binding and Conformational Change.” Ph.D., Biophysics and Biophysical Chemistry, Johns Hopkins University, 2017.
- Zhang, Liqun. “Different Dynamics and Pathway of Disulfide Bonds Reduction of Two Human Defensins, a Molecular Dynamics Simulation Study.” Proteins: Structure, Function, and Bioinformatics, January 2017. doi:10.1002/prot.25247.
- Zhang, Liqun, and Matthias Buck. “Molecular Dynamics Simulations Reveal Isoform Specific Contact Dynamics Betwe en the Plexin Rho GTPase Binding Domain (RBD) and Small Rho GTPases Rac1 and Rnd1.” The Journal of Physical Chemistry B, January 1 9, 2017. doi:10.1021/acs.jpcb.6b11022.
- Adelman, Joshua L., Chiara Ghezzi, Paola Bisignano, Donald D. F. Loo, Seungho Choe, Jeff Abramson, John M. Rose nberg, Ernest M. Wright, and Michael Grabe. “Stochastic Steps in Secondary Active Sugar Transport.” Proceedings of the National Academy of Sciences 113, no. 27 (July 5, 2016): E3960–E3966. doi:10.1073/pnas.1525378113.
- Araya, Carlos L, Can Cenik, Jason A Reuter, Gert Kiss, Vijay S Pande, Michael P Snyder, and William J Greenleaf . “Identification of Significantly Mutated Regions across Cancer Types Highlights a Rich Landscape of Functional Molecular Alterat ions.” Nature Genetics 48, no. 2: 117–25. doi:10.1038/ng.3471.
- Araya-Secchi, Raul, Brandon L. Neel, and Marcos Sotomayor. “An Elastic Element in the Protocadherin-15 Tip Link of the Inner Ear.” Nature Communications 7 (November 18, 2016): 13458. https://doi.org/10.1038/ncomms13458.
- Bennett, W. F. Drew, Chun Kit Hong, Yi Wang, and D. Peter Tieleman. “Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers.” Journal of Chemical Theory and Computation 12, no. 9 (September 13, 2016): 4524–33. doi:10.1021/acs.jctc.6b00265.
- Bhattacharya, Swati, Jejoong Yoo, and Aleksei Aksimentiev. “Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore.” ACS Nano 10, no. 4 (April 26, 2016): 4644–51. doi:10.1021/acsnano.6b00940.
- Boiteux, C., and T.W. Allen. “Chapter Six - Understanding Sodium Channel Function and Modulation Using Atomisti c Simulations of Bacterial Channel Structures.” In Current Topics in Membranes, edited by Robert J. French and Sergei Yu. Noskov, Volume 78:145–82. Academic Press, 2016. http://www.sciencedirect.com/science/article/pii/S1063582316300096.
- Chipot, Christophe, and Jeffrey Comer. “Subdiffusion in Membrane Permeation of Small Molecules.” Scientific Rep orts 6 (November 2, 2016): 35913. doi:10.1038/srep35913.
- Debiec, Karl T., David S. Cerutti, Lewis R. Baker, Angela M. Gronenborn, David A. Case, and Lillian T. Chong. “Further along the Road Less Traveled: AMBER Ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model.” Journal of Chemical Theory and Computation 12, no. 8 (August 9, 2016): 3926–47. https://doi.org/10.1021/acs.jctc.6b00567.
- Dewan, Sukriti, Kimberly J. McCabe, Michael Regnier, Andrew D. McCulloch, and Steffen Lindert. “Molecular Effec ts of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation—An Integrated Multiscale Modeling Study.” The Journal o f Physical Chemistry B 120, no. 33 (August 25, 2016): 8264–75. doi:10.1021/acs.jpcb.6b01950.
- Dhakshnamoorthy, Balasundaresan, Ahmed Rohaim, Huan Rui, Lydia Blachowicz, and Benoît Roux. “Structural and Fun ctional Characterization of a Calcium-Activated Cation Channel from Tsukamurella Paurometabola.” Nature Communications 7 (Septembe r 28, 2016): 12753. doi:10.1038/ncomms12753.
- Eskici, Gözde, and Paul H. Axelsen. “The Size of AOT Reverse Micelles.” The Journal of Physical Chemistry B, October 28, 2016. doi:10.1021/acs.jpcb.6b06420.
- Gaieb, Zied, David D. Lo, and Dimitrios Morikis. “Molecular Mechanism of Biased Ligand Conformational Changes i n CC Chemokine Receptor 7.” Journal of Chemical Information and Modeling 56, no. 9 (September 26, 2016): 1808–22. doi:10.1021/acs. jcim.6b00367.
- Gibbs, Eric B., and Scott A. Showalter. “Quantification of Compactness and Local Order in the Ensemble of the I ntrinsically Disordered Protein FCP1.” The Journal of Physical Chemistry B 120, no. 34 (September 2016): 8960–69. doi:10.1021/acs. jpcb.6b06934.
- Hu, Xiaohu. “Complex Non-Equilibrium Structural Dynamics in Globular Proteins.” Ph.D., University of Tennessee -Knoxville, 2016. http://trace.tennessee.edu/utk_graddis s/3707.
- Hu, Xiaohu, Liang Hong, Micholas Dean Smith, Thomas Neusius, Xiaolin Cheng, and Jeremy C. Smith. “The Dynamics of Single Protein Molecules Is Non-Equilibrium and Self-Similar over Thirteen Decades in Time.” Nature Physics 12, no. 2 (201 6): 171–74. doi:10.1038/nphys3553.
- Huang, Jing, Sirish Kaushik Lakkaraju, Andrew Coop, and Alexander D. MacKerell. “Conformational Heterogeneity of Intracellular Loop 3 of the μ-Opioid G-Protein Coupled Receptor.” The Journal of Physical Chemistry B 120, no. 46 (November 23, 2016): 11897–904. https://doi.org/10.1021/acs.jpcb.6b09351.
- Huang, Tran, Rodgers, Bartlett, Hemley, and Ichiye. “A Molecular Perspective on the Limits of Life: Enzymes und er Pressure.” Condensed Matter Physics 19, no. 2 (March 2016): 22801. doi:10.5488/CMP.19.22801.
- Interlandi, Gianluca, and Wendy E. Thomas. “Mechanism of Allosteric Propagation across a Β-Sheet Structure Inve stigated by Molecular Dynamics Simulations: Β-Sheet Allosteric Mechanism.” Proteins: Structure, Function, and Bioinformatics 84, n o. 7 (July 2016): 990–1008. doi:10.1002/prot.25050.
- Khelashvili, George, Solveig Gaarde Schmidt, Lei Shi, Jonathan A. Javitch, Ulrik Gether, Claus J. Loland, and H arel Weinstein. “Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na + and K + Ions and the Protonation Sta te of Glu 290.” Journal of Biological Chemistry 291, no. 38 (September 16, 2016): 19786–99. doi:10.1074/jbc.M116.731455.
- LeVine, Michael V., Michel A. Cuendet, George Khelashvili, and Harel Weinstein. “Allosteric Mechanisms of Molec ular Machines at the Membrane: Transport by Sodium-Coupled Symporters.” Chemical Reviews 116, no. 11 (June 8, 2016): 6552–87. doi: 10.1021/acs.chemrev.5b00627.
- Lin, Xingcheng, Jeffrey K. Noel, Qinghua Wang, Jianpeng Ma, and José N. Onuchic. “Lowered pH Leads to Fusion Pe ptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin.” The Journal of Physical Chemistry B 120, no. 36 (Sept ember 15, 2016): 9654–60. doi:10.1021/acs.jpcb.6b06775.
- Medovoy, David, Eduardo Perozo, and Benoît Roux. “Multi-Ion Free Energy Landscapes Underscore the Microscopic M echanism of Ion Selectivity in the KcsA Channel.” Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, no. 7 (July 2016): 1722 –32. doi:10.1016/j.bbamem.2016.02.019.
- Metzler, Ralf. “Protein Physics: Forever Ageing.” Nature Physics, November 23, 2015. doi:10.1038/nphys3585.
- Monje-Galvan, Viviana, and Jeffery B. Klauda. “Peripheral Membrane Proteins: Tying the Knot between Experiment and Computation.” New Approaches for Bridging Computation and Experiment on Membrane Proteins 1858, no. 7, Part B (July 2016): 158 4–93. doi:10.1016/j.bbamem.2016.02.018.
- Mugnai, Mauro L., and D. Thirumalai. “Kinematics of the Lever Arm Swing in Myosin VI.” Proceedings of the National Academy of Sciences 114, no. 22 (May 30, 2017): E4389–98. https://doi.org/10.1073/pnas.1615708114.
- Perrin, B. Scott, Jr., Riqiang Fu, Myriam L. Cotten, and Richard W. Pastor. “Simulations of Memb rane-Disrupting Peptides II: AMP Piscidin 1 Favors Surface Defects over Pores.” Biophysical Journal 111, no. 6 (n.d.): 1258–66. Ac cessed October 10, 2016. doi:10.1016/j.bpj.2016.08.015.
- Perrin, B. Scott, Jr., and Richard W. Pastor. “Simulations of Membrane-Disrupting Peptides I: Alameth icin Pore Stability and Spontaneous Insertion.” Biophysical Journal 111, no. 6 (n.d.): 1248–57. Accessed October 10, 2016. doi:10. 1016/j.bpj.2016.08.014.
- Pino-Angeles A, Leveritt JM III and Lazaridis T (2105) Pore structure and synergy in antimicrobial peptides of the magainin family. PLOS comp Biol. 12(1): e1004570. doi:10.1371/journal.pcbi.1004570
- Qi, Yifei, Sunhwan Jo, and Wonpil Im. “Roles of Glycans in Interactions between gp120 and HIV Broadly Neutraliz ing Antibodies.” Glycobiology, November 3, 2015, cwv101. doi:10.1093/glycob/cwv101.
- Raveh, Barak, Jerome M. Karp, Samuel Sparks, Kaushik Dutta, Michael P. Rout, Andrej Sali, and David Cowburn. “S lide-and-Exchange Mechanism for Rapid and Selective Transport through the Nuclear Pore Complex.” Proceedings of the National Academy of Sciences 113, no. 18 (May 3, 2016): E2489–E2497. doi:10.1073/pnas.1522663113.
- Rivalta, Ivan, George P. Lisi, Ning-Shiuan Snoeberger, Gregory A Manley, J. Patrick Loria, and Victor S. Batist a. “Allosteric Communication Disrupted by Small Molecule Binding to the Imidazole Glycerol Phosphate Synthase Protein-Protein Inte rface.” Biochemistry, October 31, 2016. doi:10.1021/acs.biochem.
- Rui, Huan, Pablo Artigas, and Benoît Roux. “The Selectivity of the Na + /K + -Pump Is Controlled by Binding Sit e Protonation and Self-Correcting Occlusion.” eLife 5 (August 4, 2016). doi:10.7554/eLife.16616.
- Schiffer, Jamie M., Victoria A. Feher, Robert D. Malmstrom, Roxana Sida, and Rommie E. Amaro. “Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A.” Biophysical Journal 111, no. 8 (October 2016): 1631–40. https://doi.org/10.1016/j.bpj.2016.08.041.
- Schneider, Sebastian, Davide Provasi, and Marta Filizola. “How Oliceridine (TRV-130) Binds and Stabilizes a μ-Opioid Receptor Conformational State That Selectively Triggers G Protein Signaling Pathways.” Biochemistry 55, no. 46 (November 22, 2016): 6456–66. https://doi.org/10.1021/acs.biochem.6b00948.
- Sodt, A.J., R.M. Venable, E. Lyman, and R.W. Pastor. “Nonadditive Compositional Curvature Energetics of Lipid B ilayers.” Phys. Rev. Lett 117, no. 13 (2016): 138104. doi:10.1103/PhysRevLett.117.138104.
- Stolzenberg, Sebastian, Mayako Michino, Michael V. LeVine, Harel Weinstein, and Lei Shi. “Computational Approaches to Detect Allosteric Pathways in Transmembrane Molecular Machines.” Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, no. 7 (July 2016): 1652–62. https://doi.org/10.1016/j.bbamem.2016.01.010.
- Vermaas, J.V., N. Trebesch, C.G. Mayne, S. Thangapandian, M. Shekhar, P. Mahinthichaichan, J.L. Baylon, et al. “Chapter Sixteen - Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.” In Methods in Enzymology, edited by Gregory A. Voth, Volume 578:373–428. Academic Press, 2016. http://www.sciencedirect.com/science/article/pii/S0076687916300775.
- Wu, Emilia L., Yifei Qi, Soohyung Park, Sairam S. Mallajosyula, Alexander D. MacKerell, Jeffery B. Klauda, and Wonpil Im. “Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein.” Biophysical Journal 109, no. 10 (November 201 5): 2090–2100. doi:10.1016/j.bpj.2015.10.009
- Yelshanskaya, Maria V., Appu K. Singh, Jared M. Sampson, Chamali Narangoda, Maria Kurnikova, and Alexander I. Sobolevsky. “Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs.” Neuron 91, no. 6 (September 2016): 1305–15. https://doi.org/10.1016/j.neuron.2016.08.012.
- Yuan, Shuguang, Qian Peng, Krzysztof Palczewski, Horst Vogel, and Slawomir Filipek. “Mechanistic Studies on the Stereoselectivity of the Serotonin 5-HT 1A Receptor.” Angewandte Chemie International Edition 55, no. 30 (July 18, 2016): 8661–65 . doi:10.1002/anie.201603766.
- Yuan, Shuguang, H. C. Stephen Chan, Horst Vogel, Slawomir Filipek, Raymond C. Stevens, and Krzysztof Palczewski. “The Molecular Mechanism of P2Y 1 Receptor Activation.” Angewandte Chemie International Edition 55, no. 35 (August 22, 2016): 10331–35. https://doi.org/10.1002/anie.201605147.
- Zhang, Liqun, Susmita Borthakur, and Matthias Buck. “Dissociation of a Dynamic Protein Complex Studied by All-A tom Molecular Simulations.” Biophysical Journal 110, no. 4 (n.d.): 877–86. Accessed October 10, 2016. doi:10.1016/j.bpj.2015.12.03 6.
- Zhang, Yi, Klaus Schulten, Martin Gruebele, Paramjit S. Bansal, David Wilson, and Norelle L. Daly. “D isulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide.” Biophysical Journal 110, no. 8 (April 2016): 174 4–52. doi:10.1016/j.bpj.2016.03.027.
- Zhang, Yuliang, Mohtadin Hashemi, Zhengjian Lv, and Yuri L. Lyubchenko. “Self-Assembly of the Full-Length Amylo id Aβ42 Protein in Dimers.” Nanoscale, 2016. doi:10.1039/C6NR06850B.
- Bergonzo C, Henriksen N, Roe DR, and Cheatham, TE III (2015) Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields. RNA 29, 1578-1590.
- Bykhovskaia M (2015) Calcium Binding Promotes Conformational Flexibility of the Neuronal Ca 2+ Sensor Synaptotagmin. Biophysical journal 108.10: 2507-2520.
- Caliman AD, Swift SE, Wang Y, Miao, Y, McCammon JA, (2015). Investigation of the conformational dynamics of the apo A2A adenosine receptor. Protein Sci. 24, 1004-1012. PMCID: PMC4456113
- Castillo JP, Rui H, Basilio D, Das A, Roux B, Latorre R, Bezanilla F, Holmgren M (2015) Mechanism of potassium ion uptake by the Na(+)/K(+)-ATPase. Nat Commun. Jul 24 6:7622. doi: 10.1038/ncomms8622.
- Cheatham TE III and Roe DR (2015) The impact of heterogeneous computing on workflows for biomolecular simulation and analysis. Computing in Science and Engineering 17:2, 30-39.
- Cheatham, Thomas E., and David A. Case. “Twenty-Five Years of Nucleic Acid Simulations.” Biopolymers, June 2013, 969–77. https://doi.org/10.1002/bip.22331.
- Cheng, Mary Hongying, and Ivet Bahar. “Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter.” Structure 23, no. 11 (November 2015): 2171–81. https://doi.org/10.1016/j.str.2015.09.001.
- Chen Y, Bauer BW, Rapoport TA, and Gumbart JC (2015) Conformational changes of the clamp of the protein translocation ATPase SecA. Journal of Molecular Biology. 427:2348-2359.
- Cheng X, Jo S, Qi Y, Marassi, FM, and Im W (2015) Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes. Biophysical J. 108(8), 1954-1962.
- Chenyu W, and Pohorille A (2015) M2 Proton Channel: Toward a Model of a Primitive Proton Pump. Origins of Life and Evolution of Biospheres 1-8.
- Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, Del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN (2015) Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. The Journal of Membrane Biology 248, no. 4: 611-640.
- Duan M, Liu H, Li M, and Huo S (2015). Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562. The Journal of Chemical Physics, 143(13), 135101.
- Flores-Canales JC and Kurnikova M (2015) Microsecond Simulations of the Diphtheria Toxin Translocation Domain in Association with Anionic Lipid Bilayers. The Journal of Physical Chemistry B 119 (36) 12074–12085 DOI: 10.1021/acs.jpcb.5b07909
- Flores-Canales JC and Kurnikova M. (2015) Targeting Electrostatic Interactions in Accelerated Molecular Dynamics with Application to Protein Partial Unfolding. Journal of Chemical Theory and Computation 11 (6), 2550–2559, DOI: 10.1021/ct501090y
- Flores-Canales JC, Vargas-Uribe M, Ladokhin AS, and Kurnikova M (2015) Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment. The Journal of membrane biology 248(3). DOI: 10.1007/s00232-015-9771-3.
- Freites JA, and Tobias DJ (2015) Voltage Sensing in Membranes: From Macroscopic Currents to Molecular Motions. The Journal of membrane biology 1-12.
- Galindo-Murillo R, Roe DR, and Cheatham TE III (2015) Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). Biochimica Biophys. Acta 1850, 1041-1058 doi: 10.1016/j.bbagen.2014.09.007.
- Ghatak C, Rodnn MV, Vargas-Uribe M, McCluskey AJ, Flores-Canales JC, Kurnikova M and Ladokhin AS. (2015) Role of Acidic Residues in Helices TH8–TH9 in Membrane Interactions of the Diphtheria Toxin T Domain. Toxins 7(4),1303-1323.
- Gill RL Jr., Castaing J-P, Hsin J, Tan IS, Wang X, Huang KC, Tian F and Ramamurthi KS (2015) Structural and mechanistic basis for the geometric cue-driven subcellular localization of a bacterial protein”, PNAS 112 E1908-E1915.
- Gołaś EI, Czaplewski C, Scheraga HA and Liwo, A. (2015) Common functionally important motions of the nucleotide‐binding domain of Hsp70. Proteins: Structure, Function, and Bioinformatics 83.2: 282-299.
- Gur M, Zomot E, Cheng MH, and Bahar I. (2015). Energy landscape of LeuT from molecular simulations. The Journal of Chemical Physics, 143(24), 243134.
- Hardy DJ, Wu Z, Phillips JC, Stone JE, Skeel RD and Schulten K (2015) Multilevel summation method for electrostatic force evaluation. Journal of chemical theory and computation, 11(2), 766-779.
- Hu X, Hong L, Smith M, Neusius T, Cheng X and Smith J (2015) The Dynamics of Single Protein Molecules is Nonequilibrium and Self-Similar over Thirteen Decades in Time. Nature Physics 12, 171-174.
- Jo, Sunhwan, Yifei Qi, and Wonpil Im. “Preferred Conformations of N -Glycan Core Pentasaccharide in Solution and in Glycoproteins.” Glycobiology, September 24, 2015, cwv083. doi:10.1093/glycob/cwv083.
- Lee HS, Qi Y and Im W (2015) Effects of N-glycosylation on Protein Conformation and Dynamics: Protein Data Bank Analysis and Molecular Dynamics Simulation Study. Sci. Rep. 5:8926.
- Lee S, Bhattacharya S, Tate CG, Grisshammer R and Vaidehi N (2015) Structural Dynamics and Thermostabilization of Neurotensin Receptor 1. The Journal of Physical Chemistry B, 119(15), 4917-4928.
- Leveritt JM, Pino-Angeles A, and Lazaridis T (2015) The Structure of a Melittin-Stabilized Pore. Biophysical Journal 108.10: 2424-2426.
- Li J, Wen PC, Moradi M and Tajkhorshid E (2015) Computational characterization of structural dynamics underlying function in active membrane transporters. Current opinion in structural biology, 31, 96-105.
- Li Q, Rong Shen R, Treger, JS, Wanderling SS, Milewski W, Siwowska K, Bezanilla F and Perozo E. Resting state of the human proton channel dimer in a lipid bilayer Proc Natl Acad Sci U S A. 2015 Nov 3 112(44):E5926-35. doi: 10.1073/pnas.1515043112.1515043112.
- Malmstrom RD, Kornev AP, Taylor SS and Amaro RE (2015) Allostery through the computational microscope: cAMP activation of a canonical signalling domain. Nature communications, 6.
- Martin DR and Matyushov DV (2015) Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex. The Journal of chemical physics, 142(16), 161101.
- Martin DR and Matyushov DV (2015) Photosynthetic diode: electron transport rectification by wetting the quinone cofactor. Physical Chemistry Chemical Physics, 17(35), 22523-22528.
- Mouchlis VD, Bucher D , McCammon JA and Dennis EA (2015) Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates. Proceedings of the National Academy of Sciences, 112(6), E516-E525. See the movies at: http://health.ucsd.edu/news/releases/Pages/2015-01-26-3D-enzyme-model-tool-for-drug-development.aspx https://sciencenode.org/feature/enzymes-prove-no-match-supercomputers.php
- Nanda H, Heinrich F and Lösche M (2015) Membrane association of the PTEN tumor suppressor: Neutron scattering and MD simulations reveal the structure of protein–membrane complexes. Methods 77: 136-146.
- Osuna S, Jiménez-Osés G, Noey, EL and Houk KN (2015) Molecular Dynamics Explorations of Active Site Structure in Designed and Evolved Enzymes. Accounts of chemical research, 48(4), 1080-1089.
- Pontiggia F, Pachov DV, Clarkson MW, Villali J, Hagan M, Pande VS and Kern D (2015) Free energy landscape of activation in a signalling protein at atomic resolution. Nature communications, 6.
- Shan Y and Al-Hashimi HM (2015) Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs. The Journal of Physical Chemistry B 119.30: 9614-9626.
- Sharp KA, O'Brien E, Kasinath V and Wand AJ (2015) On the relationship between NMR‐derived amide order parameters and protein backbone entropy changes. Proteins: Structure, Function, and Bioinformatics, 83(5), 922-930.
- Sodt AJ, Pastor RW, Lyman E (2015) Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin, Biophysical Journal 109, 5, 948-955. doi: 10.1016/j.bpj.2015.07.036
- Wei C and Pohorille A (2015) M2 Proton Channel: Toward a Model of a Primitive Proton Pump, Orig Life Evol Biosph 45:241–248 doi: 10.1007/s11084-015-9421-x
- Wilson, MA and Pohorille A (2015) Calculating Conductance of Ion Channels–Linking Molecular Dynamics and Electrophysiology. Journal of Physics: Conference Series. Vol. 574. No. 1. IOP Publishing.
- Wilson, M.A. and Pohorille, A. (2015) Molecular Dynamics Test of an Electrodiffusion Model, J. Phys. Cof. Series 574 012009, doi:10.1088/1742-6596/574/1/012009.
- Wirth AJ, Liu Y, Prigozhin MB, Schulten K, Gruebele M (2015) Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations, J. Am. Chem. Soc. 137 (22), 7152–7159. DOI: http://pubs.acs.org/doi/full/10.1021/jacs.5b02474
- Wu EL, Qi Y, Park S, Mallajosyula SS, MacKerell Jr AD, Klauda JB and Im W (2015) Insight into Early-stage Unfolding of GPI-anchored Human Prion Protein. Biophys. J. 2015 Nov 17 109(10):2090-100. doi: 10.1016/j.bpj.2015.10.009. PMID: 26588568
- Yang, Shan, and Hashim M. Al-Hashimi. “Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.” The Journal of Physical Chemistry B 119, no. 30 (July 30, 2015): 9614–26. doi:10.1021/acs.jpcb.5b03859.
- Yuan S, Palczewski K, Peng Q, Kolinski M, Vogel H, Filipek S (2015) The mechanism of ligand-induced activation or inhibition of mu- and kappa-opioid receptors, Angew. Chem. Int. Ed. 54, 7560-7563. doi:10.1002/anie.201501742
- Yukun W, Ulmschneider JP and Zhao S (2015) How Reliable are Molecular Dynamics Simulations of Membrane Active Antimicrobial Peptides. Biophysical Journal 108.2: 78a.
- Zhang, Mingzhen, Rundong Hu, Hong Chen, Yung Chang, Xiong Gong, Fufeng Liu, and Jie Zheng. “Interfacial Interaction and Lateral Association of Cross-Seeding Assemblies between HIAPP and RIAPP Oligomers.” Phys. Chem. Chem. Phys. 17, no. 16 (2015): 10373–82. https://doi.org/10.1039/C4CP05658B.
- Zhang L, Polyansky A and Buck M (2015) Modeling Transmembrane Domain Dimers/Trimers of Plexin Receptors: Implications for Mechanisms of Signal Transmission across the Membrane, PLoS One 10(4): e0121513. doi: 10.1371/journal.pone.0121513
- Zomot E, Gur M, Bahar I (2015) Microseconds simulations reveal a new sodium-binding site and the mechanism of sodium-coupled substrate uptake by LeuT. J Biol Chem. 290(1):544-55.
Adelman, Joshua L., Ying Sheng, Seungho Choe, Jeff Abramson, Ernest M. Wright, John M. Rosenberg, and Michael Grabe. “Structural Determinants of Water Permeation through the Sodium-Galactose Transporter VSGLT.” Biophysical Journal 106, no. 6 (March 2014): 1280–89. https://doi.org/10.1016/j.bpj.2014.01.006.
Baker, Michelle K., and Cameron F. Abrams. “Dynamics of Lipids, Cholesterol, and Transmembrane α-Helices from Microsecond Molecular Dynamics Simulations.” The Journal of Physical Chemistry B 118, no. 47 (November 26, 2014): 13590–600. https://doi.org/10.1021/jp507027t.
Boiteux, C., I. Vorobyov, R. J. French, C. French, V. Yarov-Yarovoy, and T. W. Allen. “Local Anesthetic and Antiepileptic Drug Access and Binding to a Bacterial Voltage-Gated Sodium Channel.” Proceedings of the National Academy of Sciences 111, no. 36 (September 9, 2014): 13057–62. https://doi.org/10.1073/pnas.1408710111.
Boiteux, Céline, Igor Vorobyov, and Toby W. Allen. “Ion Conduction and Conformational Flexibility of a Bacterial Voltage-Gated Sodium Channel.” Proceedings of the National Academy of Sciences 111, no. 9 (March 4, 2014): 3454–59. https://doi.org/10.1073/pnas.1320907111.
Choudhary, Om P, Aviv Paz, Joshua L Adelman, Jacques-Philippe Colletier, Jeff Abramson, and Michael Grabe. “Structure-Guided Simulations Illuminate the Mechanism of ATP Transport through VDAC1.” Nature Structural & Molecular Biology 21, no. 7 (June 8, 2014): 626–32. https://doi.org/10.1038/nsmb.2841.
Debiec, Karl T., Angela M. Gronenborn, and Lillian T. Chong. “Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields.” The Journal of Physical Chemistry B 118, no. 24 (June 19, 2014): 6561–69. https://doi.org/10.1021/jp500958r.
Galindo-Murillo, Rodrigo, Daniel R. Roe, and Thomas E. Cheatham. “On the Absence of Intrahelical DNA Dynamics on the Μs to Ms Timescale.” Nature Communications 5 (October 29, 2014): 5152. https://doi.org/10.1038/ncomms6152.
Hong, Chunkit, D. Peter Tieleman, and Yi Wang. “Microsecond Molecular Dynamics Simulations of Lipid Mixing.” Langmuir 30, no. 40 (October 14, 2014): 11993–1. https://doi.org/10.1021/la502363b.
- Houk, KN. “Computational Enzyme Design and Methods to Predict the Role of Remote Mutations. In New Chemistry and New Opportunities from the Expanding Protein Universe.” In Proceedings of the 23rd International Solvay Conference on Chemistry., 50:70. World Scientific, 2014. https://books.google.com/books?hl=en&lr=&id=4hC3CgAAQBAJ&oi=fnd&pg=PA70&dq=Computational+Enzyme+Design+and+Methods+to+predict+the+role+of+Remote+Mutations&ots=AFxIrrbMin&sig=U7B5Xq_1btluir4qVzrO3_A1FWQ#v=onepage&q=Computational%20Enzyme%20Design%20and%20Methods%20to%20predict%20the%20role%20of%20Remote%20Mutations&f=false.
Jiménez-Osés, Gonzalo, Sílvia Osuna, Xue Gao, Michael R Sawaya, Lynne Gilson, Steven J Collier, Gjalt W Huisman, Todd O Yeates, Yi Tang, and K N Houk. “The Role of Distant Mutations and Allosteric Regulation on LovD Active Site Dynamics.” Nature Chemical Biology 10, no. 6 (April 13, 2014): 431–36. https://doi.org/10.1038/nchembio.1503.
Li, Qufei, Sherry Wanderling, Marcin Paduch, David Medovoy, Abhishek Singharoy, Ryan McGreevy, Carlos A Villalba-Galea, et al. “Structural Mechanism of Voltage-Dependent Gating in an Isolated Voltage-Sensing Domain.” Nature Structural & Molecular Biology 21, no. 3 (February 2, 2014): 244–52. https://doi.org/10.1038/nsmb.2768.
Liu, Yanxin, Maxim B. Prigozhin, Klaus Schulten, and Martin Gruebele. “Observation of Complete Pressure-Jump Protein Refolding in Molecular Dynamics Simulation and Experiment.” Journal of the American Chemical Society 136, no. 11 (March 19, 2014): 4265–72. https://doi.org/10.1021/ja412639u.
Malmstrom, Robert D., Christopher T. Lee, Adam T. Van Wart, and Rommie E. Amaro. “Application of Molecular-Dynamics Based Markov State Models to Functional Proteins.” Journal of Chemical Theory and Computation 10, no. 7 (July 8, 2014): 2648–57. https://doi.org/10.1021/ct5002363.
McClendon, C. L., A. P. Kornev, M. K. Gilson, and S. S. Taylor. “Dynamic Architecture of a Protein Kinase.” Proceedings of the National Academy of Sciences 111, no. 43 (October 28, 2014): E4623–31. https://doi.org/10.1073/pnas.1418402111.
Monroe, Jacob I., Walid G. El-Nahal, and Michael R. Shirts. “Investigating the Mutation Resistance of Nonnucleoside Inhibitors of HIV-RT Using Multiple Microsecond Atomistic Simulations: Microsecond Simulations of HIV-RT Inhibition.” Proteins: Structure, Function, and Bioinformatics 82, no. 1 (January 2014): 130–44. https://doi.org/10.1002/prot.24346.
Noinaj, Nicholas, Adam J. Kuszak, Curtis Balusek, James C. Gumbart, and Susan K. Buchanan. “Lateral Opening and Exit Pore Formation Are Required for BamA Function.” Structure 22, no. 7 (July 2014): 1055–62. https://doi.org/10.1016/j.str.2014.05.008.
Provasi, Davide, Ana Negri, Barry S. Coller, and Marta Filizola. “Talin-Driven inside-out Activation Mechanism of Platelet ΑIIbβ3 Integrin Probed by Multimicrosecond, All-Atom Molecular Dynamics Simulations: Long-Scale MD of the Integrin-Talin Complex.” Proteins: Structure, Function, and Bioinformatics 82, no. 12 (December 2014): 3231–40. https://doi.org/10.1002/prot.24540.
Rui, Huan, Kyle T. Root, Jinwoo Lee, Kerney Jebrell Glover, and Wonpil Im. “Probing the U-Shaped Conformation of Caveolin-1 in a Bilayer.” Biophysical Journal 106, no. 6 (March 2014): 1371–80. https://doi.org/10.1016/j.bpj.2014.02.005.
Sharp, Kim A., Vignesh Kasinath, and A. Joshua Wand. “Banding 2of NMR-Derived Methyl Order Parameters: Implications for Protein Dynamics: Banding of Methyl-Bearing Side Chain Motion.” Proteins: Structure, Function, and Bioinformatics 82, no. 9 (September 2014): 2106–17. https://doi.org/10.1002/prot.24566.
Showalter, Scott A. “Intrinsically Disordered Proteins: Methods for Structure and Dynamics Studies.” In EMagRes, edited by Robin K. Harris and Roderick L. Wasylishen, 181–90. Chichester, UK: John Wiley & Sons, Ltd, 2014. http://doi.wiley.com/10.1002/9780470034590.emrstm1360.
Sodt, Alexander J., Michael Logan Sandar, Klaus Gawrisch, Richard W. Pastor, and Edward Lyman. “The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers.” Journal of the American Chemical Society 136, no. 2 (January 15, 2014): 725–32. https://doi.org/10.1021/ja4105667.
Tronin, Andrey Y., C. Erik Nordgren, Joseph W. Strzalka, Ivan Kuzmenko, David L. Worcester, Valeria Lauter, J. Alfredo Freites, Douglas J. Tobias, and J. Kent Blasie. “Direct Evidence of Conformational Changes Associated with Voltage Gating in a Voltage Sensor Protein by Time-Resolved X-Ray/Neutron Interferometry.” Langmuir 30, no. 16 (April 29, 2014): 4784–96. https://doi.org/10.1021/la500560w.
Venable, Richard M., Alexander J. Sodt, Brent Rogaski, Huan Rui, Elizabeth Hatcher, Alexander D. MacKerell, Richard W. Pastor, and Jeffery B. Klauda. “CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature.” Biophysical Journal 107, no. 1 (July 2014): 134–45. https://doi.org/10.1016/j.bpj.2014.05.034.
Villali, Janice, Francesco Pontiggia, Michael W. Clarkson, Michael F. Hagan, and Dorothee Kern. “Evidence Against the ‘Y–T Coupling’ Mechanism of Activation in the Response Regulator NtrC.” Journal of Molecular Biology 426, no. 7 (April 2014): 1554–67. https://doi.org/10.1016/j.jmb.2013.12.027.
Vorobyov, Igor, Timothy E. Olson, Jung H. Kim, Roger E. Koeppe, Olaf S. Andersen, and Toby W. Allen. “Ion-Induced Defect Permeation of Lipid Membranes.” Biophysical Journal 106, no. 3 (February 2014): 586–97. https://doi.org/10.1016/j.bpj.2013.12.027.
Wang, Connie Y., and Thomas F. Miller. “Allosteric Response and Substrate Sensitivity in Peptide Binding of the Signal Recognition Particle.” Journal of Biological Chemistry 289, no. 44 (October 31, 2014): 30868–79. https://doi.org/10.1074/jbc.M114.584912.
Wang, Qiuming, Guizhao Liang, Mingzhen Zhang, Jun Zhao, Kunal Patel, Xiang Yu, Chao Zhao, et al. “De Novo Design of Self-Assembled Hexapeptides as β-Amyloid (Aβ) Peptide Inhibitors.” ACS Chemical Neuroscience 5, no. 10 (October 15, 2014): 972–81. https://doi.org/10.1021/cn500165s.
Wang, Yukun, Tangzheng Zhao, Dongqing Wei, Erik Strandberg, Anne S. Ulrich, and Jakob P. Ulmschneider. “How Reliable Are Molecular Dynamics Simulations of Membrane Active Antimicrobial Peptides?” Biochimica et Biophysica Acta (BBA) - Biomembranes 1838, no. 9 (September 2014): 2280–88. https://doi.org/10.1016/j.bbamem.2014.04.009.
Wei, Chenyu, and Andrew Pohorille. “Flip-Flop of Oleic Acid in a Phospholipid Membrane: Rate and Mechanism.” The Journal of Physical Chemistry B 118, no. 45 (November 13, 2014): 12919–26. https://doi.org/10.1021/jp508163e.
Weingarth, Markus, Elwin A. W. van der Cruijsen, Jared Ostmeyer, Sylke Lievestro, Benoît Roux, and Marc Baldus. “Quantitative Analysis of the Water Occupancy around the Selectivity Filter of a K + Channel in Different Gating Modes.” Journal of the American Chemical Society 136, no. 5 (February 5, 2014): 2000–2007. https://doi.org/10.1021/ja411450y.
Wilson, Michael A., Thuy Hien Nguyen, and Andrew Pohorille. “Combining Molecular Dynamics and an Electrodiffusion Model to Calculate Ion Channel Conductance.” The Journal of Chemical Physics 141, no. 22 (December 14, 2014): 22D519. https://doi.org/10.1063/1.4900879.
Zhang, Mingzhen, Rundong Hu, Guizhao Liang, Yung Chang, Yan Sun, Zhenmeng Peng, and Jie Zheng. “Structural and Energetic Insight into the Cross-Seeding Amyloid Assemblies of Human IAPP and Rat IAPP.” The Journal of Physical Chemistry B 118, no. 25 (June 26, 2014): 7026–36. https://doi.org/10.1021/jp5022246.
Zhao, Jun, Rundong Hu, Michele F. M. Sciacca, Jeffrey R. Brender, Hong Chen, Ayyalusamy Ramamoorthy, and Jie Zheng. “Non-Selective Ion Channel Activity of Polymorphic Human Islet Amyloid Polypeptide (Amylin) Double Channels.” Phys. Chem. Chem. Phys. 16, no. 6 (2014): 2368–77. https://doi.org/10.1039/C3CP53345J.
- Andersson M, Ulmschneider JP, Ulmschneider MB, White SH (2013) Conformational states of melittin at a bilayer interface. Biophys J 104(6):L12–L14.
- Bastidas M, Showalter SA (2013) Thermodynamic and structural determinants of differential Pdx1 binding to elements from the insulin and IAPP promoters. J Mol Biol 425(18):3360–3377.
- Bjelic S, Nivon L, Çelebi-Ölçüm N, Kiss G, Rosewall C, Lovick H, Ingalls E, Gallaher J, Seetharaman J, Lew S, Montelione G, Hunt J, Michael F, Houk KN, Baker D (2013) Computational design of enone-binding proteins with catalytic activity for the Morita–Baylis–Hillman Reaction. ACS Chem Biol, 8(4):749–757.
- Farelli JD, Gumbart JC, Akey IV, Hempstead A, Amyot W, Head JF, McKnight CJ, Isberg RR, Akey CW (2013) IcmQ in the Type 4b secretion system contains an NAD+ binding domain. Structure 21(8):1361–1373.
- Geng R, Sotomayor M, Kinder KJ, Gopal SR, Gerka-Stuyt J, Chen DH, Hardisty-Hughes RE, Ball G, Parker A, Gaudet R, Furness D, Brown SD, Corey DP, Alagramam KN (2013) Noddy, a mouse harboring a missense mutation in protocadherin-15, reveals the impact of disrupting a critical interaction site between tip-link cadherins in inner ear hair cells. J Neurosci 33(10):4395–4404.
- Gumbart JC, Roux B, Chipot C (2013) Efficient determination of protein–protein standard binding free energies from first principles, J Am Chem Soc, 9(8): 3789–3798.
- Gumbart JC, Teo I, Roux B, Schulten K (2013) Reconciling the roles of kinetic and thermodynamic factors in membrane–protein insertion. J Am Chem Soc 135(6):2291–2297.
- Gur M, Zomot E, Bahar I (2013) Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions. J Chem Phys 139(12):121912.
- Huang W, Kim J, Jha S, Aboul-ela F (2013) The impact of a ligand binding on strand migration in the SAM-I riboswitch. PLoS Comput Biol. 9(5):e1003069.
- Kasinath V, Sharp KA, Wand AJ (2013) Microscopic insights into the NMR relaxation based protein conformational entropy meter. J Am Chem Soc, 135(4):15092–15100.
- Kunze MBA, Wright DW, Werbeck ND, Kirkpatrick J, Coveney PV, Hansen DF (2013) Loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8. J Am Chem Soc 2013, 135 (47), pp 17862–17868 DOI: 10.1021/ja408184x
- Kurnikov IV, Kyrychenko A, Flores-Canales JC, Rodnin MV, Simakov N, Vargas-Uribe M, Posokhov YO, Kurnikova M, Ladokhin AS (2013) pH-triggered conformational switching of the diphtheria toxin T-domain: the roles of N-terminal histidines. J Mol Biol 425(15):2752–2764.
- Kwon T, Dowd TL, Bargiello TA (2013) The carboxyl terminal residues 220-283 are not required for voltage gating of a chimeric connexin32 hemichannel. Biophys J 105(6):1376–1382.
- Kwon T, Tang Q, Bargiello TA (2013) Voltage-dependent gating of the Cx32*43E1 hemichannel: Conformational changes at the channel entrances. J Gen Physiol 141(2):243–259.
- Li J, Enkavi G, Wen P-C, Shaikh SA, Tajkhorshid E (2013) Transient formation of water-conducting states in membrane transporters. Proc Nat Acad Sci USA 110(19):7696–7701.
- Liang G, Zhao J, Yu X, Zheng J (2014) Comparative molecular dynamics study of human islet amyloid polypeptide (IAPP) and rat IAPP oligomers. Biochemistry 52(6):1089–1100.
- McNulty R, Ulmschneider JP, Luecke H, Ulmschneider MB (2013) Mechanisms of molecular transport through the urea channel of Helicobacter pylori. Nature Commun. 4:2900:1–10. doi: 10.1038/ncomms3900
- Noel JK, Onuchic, JN, Sulkowska JI (2013) Knotting a protein in explicit solvent. J Phys Chem Lett 4(21):3570–3573.
- Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T, Buchanan SK (2013) Structural insight into the biogenesis of β-barrel membrane proteins. Nature 501(7467):385–390.
- Ortega DR, Yang C, Ames P, Baudry J, Parkinson JS, Zhulin IB (2013) A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors. Nat Commun. 2881:1–8.
- Ostmeyer J, Chakrapani S, Pan AC, Perozo E, Roux B (2013) Recovery from slow inactivation in K+ channels is controlled by water molecules. Nature 501(7465):121–124.
- Prigozhin MB, Liu Y, Wirth AJ, Kapoor S, Winter R, Schulten K, Gruebele M (2013) Misplaced helix slows down ultrafast pressure-jump protein folding. Proc Natl Acad Sci USA 110(20):8087–8092.
- Salmon L, Bascom G, Andricioaei I, Al-Hashimi HM (2013) A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: The basis for interhelical motions revealed. J Am Chem Soc, 135(14):5457–5466.
- Shaikh SA, Li J, Enkavi G, Wen P-C, Huang Z, Tajkhorshid E (2013) Visualizing functional motions of membrane transporters with molecular dynamics simulations. Biochemistry 52(4):569–587.
- Sharp K (2013) Calculation of molecular entropies using temperature Integration. J Chem Theor Comput, 9(2):1164–1172.
- Ulmschneider MB, Bagnéris C, McCusker EC, Decaen PG, Delling M, Clapham DE, Ulmschneider JP, Wallace BA (2013) Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel. Proc Natl Acad Sci USA. 110(16):6364–6369.
- Wei C, Pohorille A (2013) Activation and proton transport mechanism in influenza A M2 channel. Biophys J, 105(9):2036–2045.
- Yu, Xiang, Qiuming Wang, Qingfen Pan, Feimeng Zhou, and Jie Zheng. “Molecular Interactions of Alzheimer Amyloid-β Oligomers with Neutral and Negatively Charged Lipid Bilayers.” Physical Chemistry Chemical Physics 15, no. 23 (2013): 8878. https://doi.org/10.1039/c3cp44448a.
- Zhang L, Buck M (2013) Molecular simulations of a dynamic protein complex: role of salt-bridges and polar interactions in configurational transitions. Biophys J 105(10):2412–2417.
- Zhang, Liqun, Alexander J. Sodt, Richard M. Venable, Richard W. Pastor, and Matthias Buck. “Prediction, Refinement, and Persistency of Transmembrane Helix Dimers in Lipid Bilayers Using Implicit and Explicit Solvent/Lipid Representations: Microsecond Molecular Dynamics Simulations of ErbB1/B2 and EphA1.” Proteins: Structure, Function, and Bioinformatics 81, no. 3 (March 2013): 365–76. https://doi.org/10.1002/prot.24192.
- Zomot E, Bahar I (2013) Intracellular gating in an inward-facing state of aspartate transporter GltPh is regulated by the movements of the helical hairpin HP2. J Biol Chem 288(12):8231–8237.
- Bhattacharya S, Derrington IM, Pavlenok M, Niederweis M, Gundlach JH, Aksimentiev A (2012) Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence. ACS Nano 6(8):6960–6968.
- Freites JA, Schow EV, White SH, Tobias DJ (2012) Microscopic origin of gating current fluctuations in a potassium channel voltage sensor. Biophys J 102(11):L44–L46.
- Lindert S, Kekenes-Huskey PM, McCammon JA (2012) Long-timescale molecular dynamics simulations elucidate the dynamics and kinetics of exposure of the hydrophobic patch in troponin C. Biophys J 103(8):1784–1789.
- Liu Y, Strümpfer J, Freddolino PL, Gruebele M, Schulten K (2012) Structural characterization of λ-repressor folding from all-atom molecular dynamics simulations. J Phys Chem Lett 3(9):1117–1123.
- Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A (2012) Modeling and simulation of ion channels. Chem Rev 112(12):6250–6284.
- Razavian NS, Kamisetty H, Langmead CJ (2012) Learning generative models of molecular dynamics. BMC Genomics 13(Suppl 1):S5.
- Rogaski B, Klauda JB (2012) Membrane-binding mechanism of a peripheral membrane protein through microsecond molecular dynamics simulations. J Mol Biol 423(5)847–886.
- Sotomayor M, Weihofen WA, Gaudet R, Corey DP (2012) Structure of a force-conveying cadherin bond essential for inner-ear mechanotransduction. Nature 492(7427):128–132.
- Wan S, Wright DW, Coveney PV (2012) Mechanism of drug efficacy within the EGF receptor revealed by microsecond molecular dynamics simulation. Mol Cancer Ther 11(11):2394–2400.
- Wright DW, Wan S, Shublaq N, Zasada SJ, Coveney PV (2012) From base pair to bedside: molecular simulation and the translation of genomics to personalised medicine. Wiley Interdiscip Rev Syst Biol Med 4(6):585–589.
- Yu X, Wang Q, Lin Y, Zhao J, Zhao C, Zheng J (2012) Structure, orientation, and surface interaction of Alzheimer amyloid-β peptides on the graphite. Langmuir 28:6595–6605.
- Zhang B, Miller TF 3rd. (2012) Direct simulation of early-stage Sec-facilitated protein translocation. J Am Chem Soc 134(33):13700–1370.
- Zhang B, Miller TF 3rd. (2012) Long-timescale dynamics and the regulation of Sec-facilitated protein translocation. Cell Rep 2(4):927–937.
- Zhao J, Luo Y, Jang H, Yu X, Wei G, Nussinov R, Zheng J (2012) Probing ion channel activity of human islet amyloid polypeptide (amylin). Biochim Biophys Acta 1818(12):3121–3130.
- Ramanathan A, Agarwal PK, Kurnikova M, Langmead CJ (2010) An online approach for mining collective behaviors from molecular dynamics simulations. J Comput Biol 17(3):309–324.