Works matching AU Vijay S. Pande
Results: 54
A universal TANGO?
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- Nature Biotechnology, 2004, v. 22, n. 10, p. 1240, doi. 10.1038/nbt1004-1240
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Structural correspondence between the a-helix and the random-flight chain resolves how unfolded proteins can have native-like properties.
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- Nature Structural Biology, 2003, v. 10, n. 11, p. 955, doi. 10.1038/nsb995
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Building Markov state models with solvent dynamics.
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- BMC Bioinformatics, 2013, v. 14, n. Suppl 2, p. 1, doi. 10.1186/1471-2105-14-S2-S8
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Solving the RNA design problem with reinforcement learning.
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- PLoS Computational Biology, 2018, v. 14, n. 6, p. 1, doi. 10.1371/journal.pcbi.1006176
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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.
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- PLoS Computational Biology, 2017, v. 13, n. 7, p. 1, doi. 10.1371/journal.pcbi.1005659
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Network models for molecular kinetics and their initial applications to human health.
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- Cell Research, 2010, v. 20, n. 6, p. 622, doi. 10.1038/cr.2010.57
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Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.
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- Journal of Computational Chemistry, 2017, v. 38, n. 10, p. 740, doi. 10.1002/jcc.24745
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Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating.
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- PLoS Computational Biology, 2020, v. 16, n. 3, p. 1, doi. 10.1371/journal.pcbi.1007530
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Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes.
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- Nature Communications, 2017, v. 8, n. 2, p. 1, doi. 10.1038/s41467-016-0015-8
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Corrigendum: Conformational heterogeneity of the calmodulin binding interface.
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- Nature Communications, 2016, v. 7, n. 8, p. 12318, doi. 10.1038/ncomms12318
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Conformational heterogeneity of the calmodulin binding interface.
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- Nature Communications, 2016, v. 7, n. 4, p. 10910, doi. 10.1038/ncomms10910
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A network of molecular switches controls the activation of the two-component response regulator NtrC.
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- Nature Communications, 2015, v. 6, n. 6, p. 7283, doi. 10.1038/ncomms8283
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Activation pathway of Src kinase reveals intermediate states as targets for drug design.
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- Nature Communications, 2014, v. 5, n. 3, p. 3397, doi. 10.1038/ncomms4397
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The Dynamic Conformational Cycle of the Group I Chaperonin C-Termini Revealed via Molecular Dynamics Simulation.
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- PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0117724
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Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel.
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- PLoS Computational Biology, 2010, v. 6, n. 10, p. 1, doi. 10.1371/journal.pcbi.1000963
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Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails.
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- PLoS Computational Biology, 2010, v. 6, n. 6, p. 1, doi. 10.1371/journal.pcbi.1000829
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Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics.
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- PLoS Computational Biology, 2007, v. 3, n. 11, p. e220, doi. 10.1371/journal.pcbi.0030220
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Computationally Discovered Potentiating Role of Glycans on NMDA Receptors.
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- Scientific Reports, 2017, p. 44578, doi. 10.1038/srep44578
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Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY.
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- Scientific Reports, 2017, p. 44116, doi. 10.1038/srep44116
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Cloud computing approaches for prediction of ligand binding poses and pathways.
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- Scientific Reports, 2015, p. 7918, doi. 10.1038/srep07918
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Discovery of novel brain permeable and G protein-biased beta-1 adrenergic receptor partial agonists for the treatment of neurocognitive disorders.
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- PLoS ONE, 2017, v. 12, n. 7, p. 1, doi. 10.1371/journal.pone.0180319
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Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.
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- Journal of Computational Chemistry, 2010, v. 31, n. 6, p. 1268, doi. 10.1002/jcc.21413
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PAPER—Accelerating parallel evaluations of ROCS.
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- Journal of Computational Chemistry, 2010, v. 31, n. 1, p. 117, doi. 10.1002/jcc.21307
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Accelerating molecular dynamic simulation on graphics processing units.
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- Journal of Computational Chemistry, 2009, v. 30, n. 6, p. 864, doi. 10.1002/jcc.21209
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Accelerating molecular dynamic simulation on the cell processor and Playstation 3.
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- Journal of Computational Chemistry, 2009, v. 30, n. 2, p. 268, doi. 10.1002/jcc.21054
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Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories.
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- Journal of Computational Chemistry, 2008, v. 29, n. 11, p. 1740, doi. 10.1002/jcc.20935
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Effects of long-range electrostatic forces on simulated protein folding kinetics.
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- Journal of Computational Chemistry, 2008, v. 29, n. 5, p. 694, doi. 10.1002/jcc.20828
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A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides.
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- Journal of Computational Chemistry, 2005, v. 26, n. 15, p. 1612, doi. 10.1002/jcc.20301
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Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling.
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- Journal of Computational Chemistry, 2005, v. 26, n. 7, p. 682, doi. 10.1002/jcc.20208
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Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation.
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- International Journal of Molecular Sciences, 2009, v. 10, n. 3, p. 1013, doi. 10.3390/ijms10031013
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Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework.
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- Biochemistry & Cell Biology, 2010, v. 88, n. 2, p. 359, doi. 10.1139/O09-187
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Assessment of the protein-structure refinement category in CASP8.
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- Proteins, 2009, v. 77, n. S9, p. 66, doi. 10.1002/prot.22538
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Simulated tempering yields insight into the low-resolution Rosetta scoring functions.
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- Proteins, 2009, v. 74, n. 3, p. 777, doi. 10.1002/prot.22210
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Increased detection of structural templates using alignments of designed sequences.
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- Proteins, 2003, v. 51, n. 3, p. 390, doi. 10.1002/prot.10346
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CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.
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- Bioinformatics, 2011, v. 27, n. 16, p. 2322, doi. 10.1093/bioinformatics/btr386
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Persistent voids: a new structural metric for membrane fusion.
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- Bioinformatics, 2007, v. 23, n. 14, p. 1753, doi. 10.1093/bioinformatics/btm250
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Absolute comparison of simulated and experimental protein-folding dynamics.
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- Nature, 2002, v. 420, n. 6911, p. 102, doi. 10.1038/nature01160
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Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.
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- Nature Immunology, 2012, v. 13, n. 12, p. 1187, doi. 10.1038/ni.2449
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Bayesian analysis of isothermal titration calorimetry for binding thermodynamics.
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- PLoS ONE, 2018, v. 13, n. 9, p. 1, doi. 10.1371/journal.pone.0203224
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Thoroughly sampling sequence space: Large-scale protein design of structural ensembles.
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- Protein Science: A Publication of the Protein Society, 2002, v. 11, n. 12, p. 2804, doi. 10.1110/ps.0203902
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Calculation of rate spectra from noisy time series data.
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- Proteins, 2012, v. 80, n. 2, p. 342, doi. 10.1002/prot.23171
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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.
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- Biopolymers, 2003, v. 68, n. 1, p. 91, doi. 10.1002/bip.10219
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Simbios: an NIH national center for physics-based simulation of biological structures.
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- Journal of the American Medical Informatics Association, 2012, v. 19, n. 2, p. 186, doi. 10.1136/amiajnl-2011-000488
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Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.
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- Nature Chemistry, 2015, v. 7, n. 9, p. 759, doi. 10.1038/nchem.2272
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Corrigendum: Discovering chemistry with an ab initio nanoreactor.
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- Nature Chemistry, 2015, v. 7, n. 1, p. 87, doi. 10.1038/nchem.2139
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Discovering chemistry with an ab initio nanoreactor.
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- Nature Chemistry, 2014, v. 6, n. 12, p. 1044, doi. 10.1038/nchem.2099
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Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.
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- Nature Chemistry, 2014, v. 6, n. 1, p. 15, doi. 10.1038/nchem.1821
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Inferring the Rate-Length Law of Protein Folding.
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- PLoS ONE, 2013, v. 8, n. 12, p. 1, doi. 10.1371/journal.pone.0078606
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SWEETLEAD: an <i>In Silico</i> Database of Approved Drugs, Regulated Chemicals, and Herbal Isolates for Computer-Aided Drug Discovery.
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- PLoS ONE, 2013, v. 8, n. 11, p. 1, doi. 10.1371/journal.pone.0079568
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Persistent Topology and Metastable State in Conformational Dynamics.
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- PLoS ONE, 2013, v. 8, n. 4, p. 1, doi. 10.1371/journal.pone.0058699
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