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.
- See the RFP
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 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.
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.
Zhang, Yi, Klaus Schulten, Martin Gruebele, Paramjit S. Bansal, David Wilson, and Norelle L. Daly. “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.
This article was featured on the cover of the Biophysical Journal.
Sodt, Alexander J., Richard W. Pastor, and Edward Lyman. “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
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.
Roll Out the Beta Barrels - Anton simulations reveal how dangerous bacteria install critical proteins, from PSC's Projects in Scientific Computing, Spring 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.
Here is a list of publications for research that made use of Anton at PSC:
- 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. https://doi.org/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. https://doi.org/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). https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/10.1007/s00232-018-0026-y.
- Hoogerheide, DP, SY Noskov, SJ Kuszak, SK Buchanan, TK Rostovtseva, and H Nanda. “Structure of VDAC-Tethered Bilayer Lipid Membranes Determined Using Neutron Reflectivity.” Acta Crystallographica D FS5160 (n.d.): in press.
- 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). https://doi.org/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. https://doi.org/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 (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. https://doi.org/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). https://doi.org/10.1038/s41467-018-05724-1.
- 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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/10.1038/s41589-018-0003-x.
- 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. https://doi.org/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. https://doi.org/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. https://doi.org/10.1073/pnas.1721181115.
- 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. https://doi.org/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. https://doi.org/10.1039/C7CP06745C.
- 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. https://doi.org/10.1016/j.str.2018.01.010.
- Taylor, Bryn C, Christopher T Lee, and Rommie E Amaro. “Structural Basis for Ligand Modulation of the CCR2 Conformational Landscape,” August 14, 2018. https://doi.org/10.1101/392068.
- Tran, Kelly. “Reduction Potential Properties of Electron Transfer Proteins.” Georgetown University, Ph.D. Thesis, 2018.
- Yu, Alvin, and Albert Y. Lau. “Glutamate and Glycine Binding to the NMDA Receptor.” Structure, June 2018. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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). https://doi.org/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). https://doi.org/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. https://doi.org/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. https://doi.org/10.1073/pnas.1706983114.
- Li, Zhen-Lu, Priyanka Prakash, and Matthias Buck. “A ‘Tug of War’ Maintains a Dynamic Protein- Membrane Complex: MD Simulations of C-Raf RBD-CRD Bound to K-Ras4B at an Anionic Membrane,” August 29, 2017. https://doi.org/10.1101/181347.
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). https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/10.1093/nar/gkx917.
- Pohorille, Andrew, Michael A. Wilson, and Gareth Shannon. “Flexible Proteins at the Origin of Life.” Life 7, no. 2 (June 5, 2017): 23. https://doi.org/10.3390/life7020023.
- 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. https://doi.org/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. https://doi.org/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). https://doi.org/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. https://doi.org/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.
- 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. https://doi.org/10.1016 /j.bpj.2017.04.042.
- 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.
- 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 Ioni c 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.
- 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 Dyna mics 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, 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.
- 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, Victoria Feher, Robert D. Malmstrom, Roxana Sida, and Rommie E. Amaro. “Capturing Invisible Mo tions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A.” Biophysical Journal , in press (2016). http://dx.doi.org/10.1016/j.bpj.2016.08.041.
- 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.
- 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, October 25, 2016. doi:10.1021/acs.biochem.6b00948.
- 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
- 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.
- 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.
- 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.
- 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 http://dx.doi.org/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. 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 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 JL, Sheng Y, Choe S, Abramson J, Wright EM, Rosenberg JM, Grabe M (2014) Structural determinants of water permeation through the sodium-galactose transporter vSGLT. Biophys J 106(6):1280–1289.
- Li Q, Wanderling S, Paduch M, Medovoy D, Singharoy A, McGreevy R, Villalba-Galea CA, Hulse RE, Roux B, Schulten K, Kossiakoff A, Perozo E (2014) Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nat Struct Mol Biol 21(3):244–252.
- Liu Y, Prigozhin MB, Schulten K, Gruebele M(2014) Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment. J Am Chem Soc 136(11):4265–4272.
- Monroe JI, El-Nahal WG, Shirts MR (2014) Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations. Proteins 82(1):130–144.
- Provasi D, Negri A, Coller BS, Filizola M (2014) Talin-driven inside-out activation mechanism of platelet αIIbβ3 integrin probed by multi-microsecond, all-atom molecular dynamics simulations. Proteins.2014 Dec 82(12):3231-40. doi: 10.1002/prot.24540. Epub 2014 Sep 25.
- Rui H, Root KT, Lee J, Glover KJ, Im W (2014) Probing the u-shaped conformation of caveolin-1 in a bilayer. Biophys J 106(6):1371–1380.
- Sharp KA, Kasinath V, Wand AJ (2014) Banding of NMR-derived methyl order parameters: Implications for protein dynamics. Proteins.2014 Sep 82(9):2106-17. doi: 10.1002/prot.24566. Epub 2014 Apr 18.
- Villali J, Pontiggia F, Clarkson MW, Hagan MF, Kern D (2014) Evidence against the "Y-T coupling" mechanism of activation in the response regulator NtrC. J Mol Biol 426(7):1554–1567.
- Weingarth M, van der Cruijsen EA, Ostmeyer J, Lievestro S, Roux B, Baldus M (2014) Quantitative analysis of the water occupancy around the selectivity filter of a K+ channel in different gating modes. J Am Chem Soc. 136(5):2000–2007.
- 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, in press
- 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. 2900:1–10.
- 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.
- Sodt AJ, Sandar ML, Gawrisch K, Pastor RW, Lyman E (2013) The molecular structure of the liquid-ordered phase of lipid bilayers. J Am Chem Soc 136(2):725–732.
- 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.
- 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.
- 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.