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.
Access to Anton 2
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
- Apply at https://grants.psc.edu/cgi-
Research conducted on Anton 1
See project summaries, including trajectory files, for some Anton 1 research.
Here are highlights of just some of the groundbreaking research enabled by Anton 1:
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 (2016): 171–74. doi:10.1038/nphys3553.
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
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 Million Little 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
Atomic-Level Characterization of the Structural Dynamics of Proteins - This paper, published in Science, details the first millisecond MD simulation on Anton.
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.
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 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).
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.
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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Pourmousa, Mohsen, and Richard Pastor. “Novel Insights to the Design of Apolipoprotein AI Mimetic Peptides.” In Biophysical Journal, 114.3:341a., 2018. (Presentation to Conference).
- 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.
- 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.
- 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.6b0 1112.
- 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, Zhenlu, 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.
- Lyman, Edward. “All-Atom Molecular Dynamics Simulation of Lipid Bilayers: Recent Successes and Current Challenges,” Vol. 62, number 4, 2017.
- 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.
- Mizuochi, T., and H. Fukasawa. “Comparative Studies on Polyguanylate Polymerase and Polyadenylate Polymerase Activities in the DNA-Dependent RNA Polymerase I Fraction from Cauliflower.” Journal of Biochemistry 79, no. 1 (January 1976): 53–60.
- 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.
- Venable, Richard M., Helgi I. Ingólfsson, Michael G. Lerner, B. Scott Perrin, Brian A. Camley, Siewert J. Marri nk, Frank L. H. Brown, and Richard W. Pastor. “Lipid and Peptide Diffusion in Bilayers: The Saffman–Delbrück Model and Periodic Bo undary Conditions.” The Journal of Physical Chemistry B, January 6, 2017. doi:10.1021/acs.jpcb.6b09111.
- 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 Ac ademy 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 Acade my 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.
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