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.
The application deadline for 2016 has passed. However, more details regarding the simulation capabilities of Anton 2 can be found in the 2016 RFP. Watch for the announcement for the next RFP, which we anticipate will be in April 2017, for allocations beginning in fall 2017.
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 1 at PSC:
- Gaieb, Zied, and Dimitrios Morikis. “Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane 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.
- Huang, Yu-ming Mindy, Mark Anthony V. Raymundo, Wei Chen, and Chia-en A. Chang. “Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease.” Biochemistry, January 6, 2017. doi:10.1021/acs.biochem.6b01112.
- Venable, Richard M., Helgi I. Ingólfsson, Michael G. Lerner, B. Scott Perrin, Brian A. Camley, Siewert J. Marrink, Frank L. H. Brown, and Richard W. Pastor. “Lipid and Peptide Diffusion in Bilayers: The Saffman–Delbrück Model and Periodic Boundary Conditions.” The Journal of Physical Chemistry B, January 6, 2017. doi:10.1021/acs.jpcb.6b09111.
- Wood, Mona L., J. Alfredo Freites, Francesco Tombola, and Douglas J. Tobias. “Atomistic Modeling of Ion Conduction 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.
- 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 Between the Plexin Rho GTPase Binding Domain (RBD) and Small Rho GTPases Rac1 and Rnd1.” The Journal of Physical Chemistry B, January 19, 2017. doi:10.1021/acs.jpcb.6b11022.
- Adelman, Joshua L., Chiara Ghezzi, Paola Bisignano, Donald D. F. Loo, Seungho Choe, Jeff Abramson, John M. Rosenberg, 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 Alterations.” 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 Ionic Current Blockade in a Biological Nanopore.” ACS Nano 10, no. 4 (April 26, 2016): 4644–51. doi:10.1021/acsnano.6b00940.
- Boiteux, C., and T.W. Allen. “Chapter Six - Understanding Sodium Channel Function and Modulation Using Atomistic 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 Reports 6 (November 2, 2016): 35913. doi:10.1038/srep35913.
- Dewan, Sukriti, Kimberly J. McCabe, Michael Regnier, Andrew D. McCulloch, and Steffen Lindert. “Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation—An Integrated Multiscale Modeling Study.” The Journal of 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 Functional Characterization of a Calcium-Activated Cation Channel from Tsukamurella Paurometabola.” Nature Communications 7 (September 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 in 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 Intrinsically 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_graddiss/3707.
- Hu, Xiaohu, Liang Hong, Micholas Dean Smith, Thomas Neusius, Xiaolin Cheng, and Jeremy C. Smith. “The Dynamics of Single Protein Molecules Is Non-Equilibrium and Self-Similar over Thirteen Decades in Time.” Nature Physics 12, no. 2 (2016): 171–74. doi:10.1038/nphys3553.
- Huang, Tran, Rodgers, Bartlett, Hemley, and Ichiye. “A Molecular Perspective on the Limits of Life: Enzymes under 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 Investigated by Molecular Dynamics Simulations: Β-Sheet Allosteric Mechanism.” Proteins: Structure, Function, and Bioinformatics 84, no. 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 Harel Weinstein. “Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na + and K + Ions and the Protonation State 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 Molecular 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 Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin.” The Journal of Physical Chemistry B 120, no. 36 (September 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 Mechanism 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): 1584–93. doi:10.1016/j.bbamem.2016.02.018.
- Perrin, B. Scott, Jr., Riqiang Fu, Myriam L. Cotten, and Richard W. Pastor. “Simulations of Membrane-Disrupting Peptides II: AMP Piscidin 1 Favors Surface Defects over Pores.” Biophysical Journal 111, no. 6 (n.d.): 1258–66. Accessed 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: Alamethicin 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 Neutralizing 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. “Slide-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. Batista. “Allosteric Communication Disrupted by Small Molecule Binding to the Imidazole Glycerol Phosphate Synthase Protein-Protein Interface.” 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 Site 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 Motions 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 Bilayers.” 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 2015): 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-Atom Molecular Simulations.” Biophysical Journal 110, no. 4 (n.d.): 877–86. Accessed October 10, 2016. doi:10.1016/j.bpj.2015.12.036.
- 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.
- Zhang, Yuliang, Mohtadin Hashemi, Zhengjian Lv, and Yuri L. Lyubchenko. “Self-Assembly of the Full-Length Amyloid 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.
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