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.
- 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.
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