Anton is a special purpose supercomputer for biomolecular simulation designed and constructed by D. E. Shaw Research (DESRES). A 512-node Anton machine has been 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.
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 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
Anton 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, the principal investigator must be a faculty or staff member at a U.S. academic or non-profit research institution.
The deadline to submit proposals for this year was June 16, 2015. Please watch this web site for an announcement of the next proposal submission opportunity. More details regarding Anton's simulation capabilities can be found in the most recent RFP.
Research conducted on Anton
Listed here is just some of the groundbreaking research enabled by Anton:
- 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 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
- 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.
- 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.
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).
Here is a list of publications for research that made use of Anton at PSC:
- Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf, WJ. Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nature Genetics 48, 117–125 (2016) doi:10.1038/ng.3471.
- Jo S, Qi Y, and Im W (2016) Preferred Conformations of N-glycan Core Pentasaccharide in Solution and in Glycoprotein. Glycobiology 26(1):19-29. doi: 10.1093/glycob/cwv083.
- 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
- 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.
- 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
- 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.
- 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.
- 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
- 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.