Works by Vijay S. Pande

Results: 54

Cloud computing approaches for prediction of ligand binding poses and pathways.

Published in:

Scientific Reports, 2015, p. 7918, doi. 10.1038/srep07918

By:

Lawrenz, Morgan;
Shukla, Diwakar;
Pande, Vijay S.

Publication type:

Article

Corrigendum: Discovering chemistry with an ab initio nanoreactor.

Published in:

Nature Chemistry, 2015, v. 7, n. 1, p. 87, doi. 10.1038/nchem.2139

By:

Wang, Lee-Ping;
Titov, Alexey;
McGibbon, Robert;
Liu, Fang;
Pande, Vijay S.;
Martínez, Todd J.

Publication type:

Article

Discovering chemistry with an ab initio nanoreactor.

Published in:

Nature Chemistry, 2014, v. 6, n. 12, p. 1044, doi. 10.1038/nchem.2099

By:

Wang, Lee-Ping;
Titov, Alexey;
McGibbon, Robert;
Liu, Fang;
Pande, Vijay S.;
Martínez, Todd J.

Publication type:

Article

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.

Published in:

Nature Chemistry, 2014, v. 6, n. 1, p. 15, doi. 10.1038/nchem.1821

By:

Kohlhoff, Kai J.;
Shukla, Diwakar;
Lawrenz, Morgan;
Bowman, Gregory R.;
Konerding, David E.;
Belov, Dan;
Altman, Russ B.;
Pande, Vijay S.

Publication type:

Article

A universal TANGO?

Published in:

Nature Biotechnology, 2004, v. 22, n. 10, p. 1240, doi. 10.1038/nbt1004-1240

By:

Pande, Vijay S.

Publication type:

Article

Increased detection of structural templates using alignments of designed sequences.

Published in:

Proteins, 2003, v. 51, n. 3, p. 390, doi. 10.1002/prot.10346

By:

Stefan M. Larson;
Amit Garg;
John R. Desjarlais;
Vijay S. Pande

Publication type:

Article

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 7, p. 1, doi. 10.1371/journal.pcbi.1005659

By:

Eastman, Peter;
Swails, Jason;
Chodera, John D.;
McGibbon, Robert T.;
Zhao, Yutong;
Beauchamp, Kyle A.;
Wang, Lee-Ping;
Simmonett, Andrew C.;
Harrigan, Matthew P.;
Stern, Chaya D.;
Wiewiora, Rafal P.;
Brooks, Bernard R.;
Pande, Vijay S.

Publication type:

Article

Persistent voids: a new structural metric for membrane fusion.

Published in:

Bioinformatics, 2007, v. 23, n. 14, p. 1753, doi. 10.1093/bioinformatics/btm250

By:

Peter M. Kasson;
Afra Zomorodian;
Sanghyun Park;
Nina Singhal;
Leonidas J. Guibas;
Vijay S. Pande

Publication type:

Article

Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation.

Published in:

International Journal of Molecular Sciences, 2009, v. 10, n. 3, p. 1013, doi. 10.3390/ijms10031013

By:

Voelz, Vincent A.;
Luttmann, Edgar;
Bowman, Gregory R.;
Pande, Vijay S.

Publication type:

Article

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

Published in:

Biopolymers, 2003, v. 68, n. 1, p. 91, doi. 10.1002/bip.10219

By:

Pande, Vijay S.;
Baker, Ian;
Chapman, Jarrod;
Elmer, Sidney P.;
Khaliq, Siraj;
Larson, Stefan M.;
Rhee, Young Min;
Shirts, Michael R.;
Snow, Christopher D.;
Sorin, Eric J.;
Zagrovic, Bojan

Publication type:

Article

Discovery of novel brain permeable and G protein-biased beta-1 adrenergic receptor partial agonists for the treatment of neurocognitive disorders.

Published in:

PLoS ONE, 2017, v. 12, n. 7, p. 1, doi. 10.1371/journal.pone.0180319

By:

Yi, Bitna;
Jahangir, Alam;
Evans, Andrew K.;
Briggs, Denise;
Ravina, Kristine;
Ernest, Jacqueline;
Farimani, Amir B.;
Sun, Wenchao;
Rajadas, Jayakumar;
Green, Michael;
Feinberg, Evan N.;
Pande, Vijay S.;
Shamloo, Mehrdad

Publication type:

Article

Thoroughly sampling sequence space: Large-scale protein design of structural ensembles.

Published in:

Protein Science: A Publication of the Protein Society, 2002, v. 11, n. 12, p. 2804, doi. 10.1110/ps.0203902

By:

Larson, Stefan M.;
England, Jeremy L.;
Desjarlais, John R.;
Pande, Vijay S.

Publication type:

Article

Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 11, p. e220, doi. 10.1371/journal.pcbi.0030220

By:

Kasson, Peter M.;
Pande, Vijay S.

Publication type:

Article

CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.

Published in:

Bioinformatics, 2011, v. 27, n. 16, p. 2322, doi. 10.1093/bioinformatics/btr386

By:

Kohlhoff, Kai J.;
Sosnick, Marc H.;
Hsu, William T.;
Pande, Vijay S.;
Altman, Russ B.

Publication type:

Article

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.

Published in:

Journal of Computational Chemistry, 2010, v. 31, n. 6, p. 1268, doi. 10.1002/jcc.21413

By:

EASTMAN, PETER;
PANDE, VIJAY S.

Publication type:

Article

PAPER—Accelerating parallel evaluations of ROCS.

Published in:

Journal of Computational Chemistry, 2010, v. 31, n. 1, p. 117, doi. 10.1002/jcc.21307

By:

HAQUE, IMRAN S.;
PANDE, VIJAY S.

Publication type:

Article

Accelerating molecular dynamic simulation on graphics processing units.

Published in:

Journal of Computational Chemistry, 2009, v. 30, n. 6, p. 864, doi. 10.1002/jcc.21209

By:

FRIEDRICHS, MARK S.;
EASTMAN, PETER;
VAIDYANATHAN, VISHAL;
HOUSTON, MIKE;
LEGRAND, SCOTT;
BEBERG, ADAM L.;
ENSIGN, DANIEL L.;
BRUNS, CHRISTOPHER M.;
PANDE, VIJAY S.

Publication type:

Article

Accelerating molecular dynamic simulation on the cell processor and Playstation 3.

Published in:

Journal of Computational Chemistry, 2009, v. 30, n. 2, p. 268, doi. 10.1002/jcc.21054

By:

Luttmann, Edgar;
Ensign, Daniel L.;
Vaidyanathan, Vishal;
Houston, Mike;
Rimon, Noam;
øland, Jeppe;
Jayachandran, Guha;
Friedrichs, Mark;
Pande, Vijay S.

Publication type:

Article

Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories.

Published in:

Journal of Computational Chemistry, 2008, v. 29, n. 11, p. 1740, doi. 10.1002/jcc.20935

By:

Monticelli, Luca;
Sorin, Eric J.;
Tieleman, D. Peter;
Pande, Vijay S.;
Colombo, Giorgio

Publication type:

Article

Effects of long-range electrostatic forces on simulated protein folding kinetics.

Published in:

Journal of Computational Chemistry, 2008, v. 29, n. 5, p. 694, doi. 10.1002/jcc.20828

By:

Robertson, Alex;
Luttmann, Edgar;
Pande, Vijay S.

Publication type:

Article

A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides.

Published in:

Journal of Computational Chemistry, 2005, v. 26, n. 15, p. 1612, doi. 10.1002/jcc.20301

By:

Sanghyun Park;
Radmer, Randall J.;
Klein, Teri E.;
Pande, Vijay S.

Publication type:

Article

Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling.

Published in:

Journal of Computational Chemistry, 2005, v. 26, n. 7, p. 682, doi. 10.1002/jcc.20208

By:

Sorin, Eric J.;
Pande, Vijay S.

Publication type:

Article

Calculation of rate spectra from noisy time series data.

Published in:

Proteins, 2012, v. 80, n. 2, p. 342, doi. 10.1002/prot.23171

By:

Voelz, Vincent A.;
Pande, Vijay S.

Publication type:

Article

Assessment of the protein-structure refinement category in CASP8.

Published in:

Proteins, 2009, v. 77, n. S9, p. 66, doi. 10.1002/prot.22538

By:

MacCallum, Justin L.;
Hua, Lan;
Schnieders, Michael J.;
Pande, Vijay S.;
Jacobson, Matthew P.;
Dill, Ken A.

Publication type:

Article

Simulated tempering yields insight into the low-resolution Rosetta scoring functions.

Published in:

Proteins, 2009, v. 74, n. 3, p. 777, doi. 10.1002/prot.22210

By:

Bowman, Gregory R.;
Pande, Vijay S.

Publication type:

Article

Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.

Published in:

Nature Immunology, 2012, v. 13, n. 12, p. 1187, doi. 10.1038/ni.2449

By:

Ring, Aaron M;
Lin, Jian-Xin;
Feng, Dan;
Mitra, Suman;
Rickert, Mathias;
Bowman, Gregory R;
Pande, Vijay S;
Li, Peng;
Moraga, Ignacio;
Spolski, Rosanne;
Özkan, Engin;
Leonard, Warren J;
Garcia, K Christopher

Publication type:

Article

Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes.

Published in:

Nature Communications, 2017, v. 8, n. 2, p. 1, doi. 10.1038/s41467-016-0015-8

By:

Ryckbosch, Steven M.;
Wender, Paul A.;
Pande, Vijay S.

Publication type:

Article

Corrigendum: Conformational heterogeneity of the calmodulin binding interface.

Published in:

Nature Communications, 2016, v. 7, n. 8, p. 12318, doi. 10.1038/ncomms12318

By:

Shukla, Diwakar;
Peck, Ariana;
Pande, Vijay S

Publication type:

Article

Conformational heterogeneity of the calmodulin binding interface.

Published in:

Nature Communications, 2016, v. 7, n. 4, p. 10910, doi. 10.1038/ncomms10910

By:

Shukla, Diwakar;
Peck, Ariana;
Pande, Vijay S.

Publication type:

Article

A network of molecular switches controls the activation of the two-component response regulator NtrC.

Published in:

Nature Communications, 2015, v. 6, n. 6, p. 7283, doi. 10.1038/ncomms8283

By:

Vanatta, Dan K.;
Shukla, Diwakar;
Lawrenz, Morgan;
Pande, Vijay S.

Publication type:

Article

Activation pathway of Src kinase reveals intermediate states as targets for drug design.

Published in:

Nature Communications, 2014, v. 5, n. 3, p. 3397, doi. 10.1038/ncomms4397

By:

Shukla, Diwakar;
Meng, Yilin;
Roux, Benoît;
Pande, Vijay S.

Publication type:

Article

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics.

Published in:

PLoS ONE, 2018, v. 13, n. 9, p. 1, doi. 10.1371/journal.pone.0203224

By:

Nguyen, Trung Hai;
Rustenburg, Ariën S.;
Krimmer, Stefan G.;
Zhang, Hexi;
Clark, John D.;
Novick, Paul A.;
Branson, Kim;
Pande, Vijay S.;
Chodera, John D.;
Minh, David D. L.

Publication type:

Article

Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework.

Published in:

Biochemistry & Cell Biology, 2010, v. 88, n. 2, p. 359, doi. 10.1139/O09-187

By:

England, Jeremy L.;
Pande, Vijay S.

Publication type:

Article

Structural correspondence between the a-helix and the random-flight chain resolves how unfolded proteins can have native-like properties.

Published in:

Nature Structural Biology, 2003, v. 10, n. 11, p. 955, doi. 10.1038/nsb995

By:

Zagrovic, Bojan;
Pande, Vijay S

Publication type:

Article

Building Markov state models with solvent dynamics.

Published in:

BMC Bioinformatics, 2013, v. 14, n. Suppl 2, p. 1, doi. 10.1186/1471-2105-14-S2-S8

By:

Chen Gu;
Huang-Wei Chang;
Maibaum, Lutz;
Pande, Vijay S.;
Carlsson, Gunnar E.;
Guibas, Leonidas J.

Publication type:

Article

Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 10, p. 1, doi. 10.1371/journal.pcbi.1000963

By:

Lucent, Del;
Snow, Christopher D.;
Aitken, Colin Echeverrı´a;
Pande, Vijay S.

Publication type:

Article

Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 6, p. 1, doi. 10.1371/journal.pcbi.1000829

By:

Kasson, Peter M.;
Lindahl, Erik;
Pande, Vijay S.

Publication type:

Article

Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.

Published in:

Nature Chemistry, 2015, v. 7, n. 9, p. 759, doi. 10.1038/nchem.2272

By:

Kohlhoff, Kai J.;
Shukla, Diwakar;
Lawrenz, Morgan;
Bowman, Gregory R.;
Konerding, David E.;
Belov, Dan;
Altman, Russ B.;
Pande, Vijay S.

Publication type:

Article

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.

Published in:

Journal of Computational Chemistry, 2017, v. 38, n. 10, p. 740, doi. 10.1002/jcc.24745

By:

Zhang, Baofeng;
Kilburg, Denise;
Eastman, Peter;
Pande, Vijay S.;
Gallicchio, Emilio

Publication type:

Article

Solving the RNA design problem with reinforcement learning.

Published in:

PLoS Computational Biology, 2018, v. 14, n. 6, p. 1, doi. 10.1371/journal.pcbi.1006176

By:

Eastman, Peter;
Shi, Jade;
Ramsundar, Bharath;
Pande, Vijay S.

Publication type:

Article

Absolute comparison of simulated and experimental protein-folding dynamics.

Published in:

Nature, 2002, v. 420, n. 6911, p. 102, doi. 10.1038/nature01160

By:

Snow, Christopher D.;
Nguyen, Houbi;
Pande, Vijay S.;
Gruebele, Martin

Publication type:

Article

Simbios: an NIH national center for physics-based simulation of biological structures.

Published in:

Journal of the American Medical Informatics Association, 2012, v. 19, n. 2, p. 186, doi. 10.1136/amiajnl-2011-000488

By:

Delp, Scott L.;
Ku, Joy P.;
Pande, Vijay S.;
Sherman, Michael A.;
Altman, Russ B.

Publication type:

Article

The Dynamic Conformational Cycle of the Group I Chaperonin C-Termini Revealed via Molecular Dynamics Simulation.

Published in:

PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0117724

By:

Dalton, Kevin M.;
Frydman, Judith;
Pande, Vijay S.

Publication type:

Article

Inferring the Rate-Length Law of Protein Folding.

Published in:

PLoS ONE, 2013, v. 8, n. 12, p. 1, doi. 10.1371/journal.pone.0078606

By:

Lane, Thomas J.;
Pande, Vijay S.

Publication type:

Article

SWEETLEAD: an <i>In Silico</i> Database of Approved Drugs, Regulated Chemicals, and Herbal Isolates for Computer-Aided Drug Discovery.

Published in:

PLoS ONE, 2013, v. 8, n. 11, p. 1, doi. 10.1371/journal.pone.0079568

By:

Novick, Paul A.;
Ortiz, Oscar F.;
Poelman, Jared;
Abdulhay, Amir Y.;
Pande, Vijay S.

Publication type:

Article

Persistent Topology and Metastable State in Conformational Dynamics.

Published in:

PLoS ONE, 2013, v. 8, n. 4, p. 1, doi. 10.1371/journal.pone.0058699

By:

Chang, Huang-Wei;
Bacallado, Sergio;
Pande, Vijay S.;
Carlsson, Gunnar E.

Publication type:

Article

Sequence Coevolution between RNA and Protein Characterized by Mutual Information between Residue Triplets.

Published in:

PLoS ONE, 2012, v. 7, n. 1, p. 1, doi. 10.1371/journal.pone.0030022

By:

Brandman, Relly;
Brandman, Yigal;
Pande, Vijay S.

Publication type:

Article

A-Site Residues Move Independently from P-Site Residues in all-Atom Molecular Dynamics Simulations of the 70S Bacterial Ribosome.

Published in:

PLoS ONE, 2012, v. 7, n. 1, p. 1, doi. 10.1371/journal.pone.0029377

By:

Brandman, Relly;
Brandman, Yigal;
Pande, Vijay S.

Publication type:

Article

Rationally Designed Turn Promoting Mutation in the Amyloid-β Peptide Sequence Stabilizes Oligomers in Solution.

Published in:

PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0021776

By:

Rajadas, Jayakumar;
Liu, Corey W.;
Novick, Paul;
Kelley, Nicholas W.;
Inayathullah, Mohammed;
LeMieux, Melburne C.;
Pande, Vijay S.

Publication type:

Article

The Roles of Entropy and Kinetics in Structure Prediction.

Published in:

PLoS ONE, 2009, v. 4, n. 6, p. 1, doi. 10.1371/journal.pone.0005840

By:

Bowman, Gregory R.;
Pande, Vijay S.

Publication type:

Article