Vijay S Pande

Vijay S Pande

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Synthesis of spiro-2,6-dioxopiperazine and spiro-2,6-dioxopyrazine scaffolds using amino acids in a three-component reaction to generate potential Sigma-1 (σ) receptor selective ligands.

Eur J Med Chem 2019 Feb 22;164:241-251. Epub 2018 Dec 22.

Department of Neurology and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, NY, USA; Center for Clinical Pharmacology, St. Louis College of Pharmacy and Washington University School of Medicine, St. Louis, MO, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ejmech.2018.12.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6361672PMC
February 2019

Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational Sampling.

Structure 2019 Jan 25;27(1):55-65.e3. Epub 2018 Oct 25.

Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive Molecular Biology Building, Room 4210, Ames, IA 50011, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2018.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318028PMC
January 2019

Note: Variational encoding of protein dynamics benefits from maximizing latent autocorrelation.

J Chem Phys 2018 Dec;149(21):216101

Department of Bioengineering, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.5043303DOI Listing
December 2018

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science.

J Chem Phys 2018 Nov;149(18):180901

Department of Chemistry, Department of Bioengineering, Department of Chemical and Biomolecular Engineering, Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, USA.

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http://aip.scitation.org/doi/10.1063/1.5052551
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http://dx.doi.org/10.1063/1.5052551DOI Listing
November 2018

PotentialNet for Molecular Property Prediction.

ACS Cent Sci 2018 Nov 2;4(11):1520-1530. Epub 2018 Nov 2.

Department of Bioengineering, Stanford University, Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acscentsci.8b00507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276035PMC
November 2018

Towards simple kinetic models of functional dynamics for a kinase subfamily.

Nat Chem 2018 Sep 9;10(9):903-909. Epub 2018 Jul 9.

Department of Bioengineering, Stanford University, Stanford, CA, USA.

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http://www.nature.com/articles/s41557-018-0077-9
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http://dx.doi.org/10.1038/s41557-018-0077-9DOI Listing
September 2018

Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors.

Biophys J 2018 Sep 28;115(5):841-852. Epub 2018 Jun 28.

Department of Bioengineering, Stanford University, Stanford, California. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.06.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127453PMC
September 2018

Automated design of collective variables using supervised machine learning.

J Chem Phys 2018 Sep;149(9):094106

Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.5029972DOI Listing
September 2018

Solving the RNA design problem with reinforcement learning.

PLoS Comput Biol 2018 06 21;14(6):e1006176. Epub 2018 Jun 21.

Department of Bioengineering, Stanford University, Stanford, CA, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6029810PMC
June 2018

Variational encoding of complex dynamics.

Phys Rev E 2018 Jun;97(6-1):062412

Biophysics Program, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1103/PhysRevE.97.062412DOI Listing
June 2018

Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems.

J Phys Chem B 2018 May 3;122(21):5291-5299. Epub 2017 Oct 3.

Department of Chemistry , Stanford University , 318 Campus Drive , Stanford , California 94305 , United States.

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http://dx.doi.org/10.1021/acs.jpcb.7b06896DOI Listing
May 2018

Transferable Neural Networks for Enhanced Sampling of Protein Dynamics.

J Chem Theory Comput 2018 Apr 19;14(4):1887-1894. Epub 2018 Mar 19.

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http://dx.doi.org/10.1021/acs.jctc.8b00025DOI Listing
April 2018

Communication: Adaptive boundaries in multiscale simulations.

J Chem Phys 2018 Apr;148(14):141104

Department of Chemistry, Department of Structural Biology, and Department of Computer Science, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.5025826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909991PMC
April 2018

A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models.

J Chem Theory Comput 2018 Feb 24;14(2):1071-1082. Epub 2018 Jan 24.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.jctc.7b01004DOI Listing
February 2018

Markov State Models: From an Art to a Science.

J Am Chem Soc 2018 02 2;140(7):2386-2396. Epub 2018 Feb 2.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jacs.7b12191DOI Listing
February 2018

Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics.

J Chem Phys 2018 Jan;148(4):044111

Department of Bioengineering, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.5005058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786450PMC
January 2018

Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core.

J Chem Theory Comput 2017 Nov 31;13(11):5496-5505. Epub 2017 Oct 31.

Department of Chemistry, ‡Department of Computer Science, and §Department of Structural Biology, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.jctc.7b00817DOI Listing
November 2017

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor-Acceptor Polymer Single Chains.

J Phys Chem Lett 2017 Nov 30;8(22):5479-5486. Epub 2017 Oct 30.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.jpclett.7b02360DOI Listing
November 2017

Note: MSM lag time cannot be used for variational model selection.

J Chem Phys 2017 Nov;147(17):176101

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.5002086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669980PMC
November 2017

Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain.

Sci Rep 2017 Nov 15;7(1):15604. Epub 2017 Nov 15.

Department of Chemistry, Stanford University, 318 Campus Drive, Stanford, California, 94305, USA.

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http://dx.doi.org/10.1038/s41598-017-10697-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5688120PMC
November 2017

Modeling the mechanism of CLN025 beta-hairpin formation.

J Chem Phys 2017 Sep;147(10):104107

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.4993207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5597441PMC
September 2017

tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables.

J Chem Theory Comput 2017 Jun 9;13(6):2440-2447. Epub 2017 May 9.

Department of Chemistry, Stanford University , 318 Campus Drive, Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.jctc.7b00182DOI Listing
June 2017

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

J Comput Chem 2017 Apr 4;38(10):740-752. Epub 2017 Feb 4.

Department of Chemistry, Brooklyn College of the City University of New York, 2900 Bedford Avenue, Brooklyn, New York, 11210.

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http://dx.doi.org/10.1002/jcc.24745DOI Listing
April 2017

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15.

J Phys Chem B 2017 04 6;121(16):4023-4039. Epub 2017 Apr 6.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.jpcb.7b02320DOI Listing
April 2017

Computationally Discovered Potentiating Role of Glycans on NMDA Receptors.

Sci Rep 2017 04 5;7:44578. Epub 2017 Apr 5.

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1038/srep44578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381272PMC
April 2017

Ward Clustering Improves Cross-Validated Markov State Models of Protein Folding.

J Chem Theory Comput 2017 Mar 17;13(3):963-967. Epub 2017 Feb 17.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.jctc.6b01238DOI Listing
March 2017

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

Nat Commun 2017 02 23;8(1). Epub 2017 Feb 23.

Departments of Chemistry and of Chemical & Systems Biology, Stanford University, Stanford, California, 94305, USA.

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http://dx.doi.org/10.1038/s41467-016-0015-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5431895PMC
February 2017

MSMBuilder: Statistical Models for Biomolecular Dynamics.

Biophys J 2017 Jan;112(1):10-15

Department of Chemistry, Stanford University, Stanford, California; Program in Biophysics, Stanford University, Stanford, California; Department of Computer Science, Stanford University, Stanford, California; Department of Structural Biology, Stanford University, Stanford, California. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2016.10.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5232355PMC
January 2017

Identification of simple reaction coordinates from complex dynamics.

J Chem Phys 2017 01;146(4):044109

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.4974306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5272828PMC
January 2017

Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field.

J Chem Theory Comput 2016 Dec 21;12(12):5960-5967. Epub 2016 Nov 21.

Department of Chemistry, University of California-Davis , Davis, California 95618, United States.

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http://dx.doi.org/10.1021/acs.jctc.6b00801DOI Listing
December 2016

Optimized parameter selection reveals trends in Markov state models for protein folding.

J Chem Phys 2016 Nov;145(19):194103

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.4967809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5116026PMC
November 2016

Transition path theory analysis of c-Src kinase activation.

Proc Natl Acad Sci U S A 2016 08 1;113(33):9193-8. Epub 2016 Aug 1.

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1602790113
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http://dx.doi.org/10.1073/pnas.1602790113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995974PMC
August 2016

Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase.

J Mol Biol 2016 Jul 14;428(13):2758-68. Epub 2016 May 14.

Department of Biochemistry, Stanford University, Beckman Center B400, Stanford, CA, 94305, USA; Department of Chemistry, Stanford University, Beckman Center B400, Stanford, CA, 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.05.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169531PMC
July 2016

Conformational heterogeneity of the calmodulin binding interface.

Nat Commun 2016 Apr 4;7:10910. Epub 2016 Apr 4.

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/ncomms10910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822001PMC
April 2016

Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.

Biophys J 2016 04;110(8):1716-1719

Department of Chemistry, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California; Structural Biology, Stanford University, Stanford, California; Department of Computer Science, Stanford University, Stanford, California. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2016.03.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850345PMC
April 2016

The dynamic conformational cycle of the group I chaperonin C-termini revealed via molecular dynamics simulation.

PLoS One 2015 30;10(3):e0117724. Epub 2015 Mar 30.

Department of Chemistry, Stanford University, Stanford, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117724PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379175PMC
February 2016

Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches.

Methods Enzymol 2015 24;557:551-72. Epub 2015 Mar 24.

Department of Chemistry, Stanford University, Stanford, California, USA; SIMBIOS NIH Center for Biomedical Computation, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1016/bs.mie.2014.12.007DOI Listing
February 2016

Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways.

J Chem Theory Comput 2016 Feb 19;12(2):638-49. Epub 2016 Jan 19.

SLAC Linear Accelerator Laboratory , Menlo Park, California 94025, United States.

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http://dx.doi.org/10.1021/acs.jctc.5b00830DOI Listing
February 2016

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations.

Nat Genet 2016 Feb 21;48(2):117-25. Epub 2015 Dec 21.

Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/ng.3471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731297PMC
February 2016

Heat dissipation guides activation in signaling proteins.

Proc Natl Acad Sci U S A 2015 Aug 3;112(33):10377-82. Epub 2015 Aug 3.

Department of Chemistry, Stanford University, Stanford, CA 94305; Simbios NIH Center for Biomedical Computation, Stanford University, Stanford, CA 94305

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http://dx.doi.org/10.1073/pnas.1501804112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547217PMC
August 2015

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

J Phys Chem B 2015 Jul 26;119(29):9423-9437. Epub 2015 Feb 26.

Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63105.

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http://dx.doi.org/10.1021/jp510896nDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772747PMC
July 2015

OpenMM: A Hardware Independent Framework for Molecular Simulations.

Comput Sci Eng 2015 Jul;12(4):34-39

Department of Chemistry, Stanford University, Stanford, CA 94305.

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http://dx.doi.org/10.1109/MCSE.2010.27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486654PMC
July 2015

United polarizable multipole water model for molecular mechanics simulation.

J Chem Phys 2015 Jul;143(1):014504

Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1063/1.4923338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499046PMC
July 2015

Efficient maximum likelihood parameterization of continuous-time Markov processes.

J Chem Phys 2015 Jul;143(3):034109

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.4926516DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514821PMC
July 2015

Percolation-like phase transitions in network models of protein dynamics.

J Chem Phys 2015 Jun;142(21):215105

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.4921989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457657PMC
June 2015

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

Nat Commun 2015 Jun 15;6:7283. Epub 2015 Jun 15.

1] Department of Chemistry, Stanford University, Stanford, California 94305, USA [2] SIMBIOS NIH Center for Biomedical Computation, Stanford University, Stanford, California 94305,USA.

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http://dx.doi.org/10.1038/ncomms8283DOI Listing
June 2015

Potential-based dynamical reweighting for Markov state models of protein dynamics.

J Chem Theory Comput 2015 Jun;11(6):2412-20

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.jctc.5b00031DOI Listing
June 2015

Inferring the rate-length law of protein folding.

PLoS One 2013 5;8(12):e78606. Epub 2013 Dec 5.

Department of Chemistry, Stanford University, Stanford, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078606PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855161PMC
March 2015

Variational cross-validation of slow dynamical modes in molecular kinetics.

J Chem Phys 2015 Mar;142(12):124105

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.4916292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398134PMC
March 2015

Entropy-production-driven oscillators in simple nonequilibrium networks.

Phys Rev E Stat Nonlin Soft Matter Phys 2015 Mar 24;91(3):032136. Epub 2015 Mar 24.

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1103/PhysRevE.91.032136DOI Listing
March 2015

Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics.

J Chem Theory Comput 2015 Mar;11(3):1094-101

Department of Chemistry, ∥Department of Computer Science, and §Department of Structural Biology, Stanford University , Stanford, California 94305, United States.

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http://pubs.acs.org/doi/10.1021/ct5010017
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http://dx.doi.org/10.1021/ct5010017DOI Listing
March 2015

Markov state models provide insights into dynamic modulation of protein function.

Acc Chem Res 2015 Feb 3;48(2):414-22. Epub 2015 Jan 3.

Department of Chemistry, ‡Biophysics Program, and §SIMBIOS, NIH Center for Biomedical Computation, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/ar5002999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333613PMC
February 2015

Modeling molecular kinetics with tICA and the kernel trick.

J Chem Theory Comput 2015 Feb;11(2):600-8

Department of Chemistry, Stanford University, Stanford, California 94305, United States

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http://dx.doi.org/10.1021/ct5007357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610300PMC
February 2015

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

Sci Rep 2015 Jan 22;5:7918. Epub 2015 Jan 22.

1] Department of Chemistry, Stanford University, Stanford, CA 94305 [2] SIMBIOS NIH Center for Biomedical Computation, Stanford University, Stanford, CA 94305.

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http://dx.doi.org/10.1038/srep07918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302315PMC
January 2015

Discovering chemistry with an ab initio nanoreactor.

Nat Chem 2014 Dec 2;6(12):1044-8. Epub 2014 Nov 2.

1] The PULSE Institute, Stanford University, Stanford, California 94305, USA [2] Department of Chemistry, Stanford University, Stanford, California 94305, USA [3] SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.

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http://dx.doi.org/10.1038/nchem.2099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239668PMC
December 2014

Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations.

J Chem Theory Comput 2014 Dec 22;10(12):5217-5223. Epub 2014 Oct 22.

Department of Chemistry, Stanford University , 318 Campus Drive, Stanford, California 94305, United States ; SIMBIOS NIH Center for Biomedical Computation and Center for Molecular Analysis and Design, Stanford University , Stanford, California 94305, United States ; SIMBIOS NIH Center for Biomedical Computation and Center for Molecular Analysis and Design, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/ct500353mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263461PMC
December 2014

Complex pathways in folding of protein G explored by simulation and experiment.

Biophys J 2014 Aug;107(4):947-55

Department of Chemistry, Stanford University, Stanford, California; Simbios Program, Stanford University, Stanford, California; Department of Structural Biology, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California; Department of Computer Science, Stanford University, Stanford, California.

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https://linkinghub.elsevier.com/retrieve/pii/S00063495140068
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http://dx.doi.org/10.1016/j.bpj.2014.06.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147789PMC
August 2014

Dynamical phase transitions reveal amyloid-like states on protein folding landscapes.

Biophys J 2014 Aug;107(4):974-82

Department of Chemistry, Stanford University, Stanford, California. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2014.06.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4142240PMC
August 2014

Statistical model selection for Markov models of biomolecular dynamics.

J Phys Chem B 2014 Jun 25;118(24):6475-81. Epub 2014 Apr 25.

Department of Chemistry, ‡Biophysics Program, §Department of Computer Science, and ∥Department of Structural Biology, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jp411822rDOI Listing
June 2014

Building Force Fields: An Automatic, Systematic, and Reproducible Approach.

J Phys Chem Lett 2014 Jun 16;5(11):1885-91. Epub 2014 May 16.

Department of Chemistry, Stanford University, Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jz500737mDOI Listing
June 2014

Introduction and overview of this book.

Adv Exp Med Biol 2014 ;797:1-6

Departments of Molecular & Cell Biology and Chemistry, University of California, Berkeley, CA, 94720, USA,

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http://dx.doi.org/10.1007/978-94-007-7606-7_1DOI Listing
April 2014

Understanding protein folding using Markov state models.

Authors:
Vijay S Pande

Adv Exp Med Biol 2014 ;797:101-6

Stanford University, Stanford, CA, 94305, USA,

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http://dx.doi.org/10.1007/978-94-007-7606-7_8DOI Listing
April 2014

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

Nat Commun 2014 Mar 3;5:3397. Epub 2014 Mar 3.

1] Department of Chemistry, Stanford University, Stanford, California 94305, USA [2] SIMBIOS NIH Center for biomedical computation, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/ncomms4397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465921PMC
March 2014

A molecular interpretation of 2D IR protein folding experiments with Markov state models.

Biophys J 2014 Mar;106(6):1359-70

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2014.02.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984984PMC
March 2014

Bayesian energy landscape tilting: towards concordant models of molecular ensembles.

Biophys J 2014 Mar;106(6):1381-90

Departments of Biochemistry and Physics and Biophysics Program, Stanford University, Stanford, California. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2014.02.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984982PMC
March 2014

Chemical kinetics and mechanisms of complex systems: a perspective on recent theoretical advances.

J Am Chem Soc 2014 Jan 2;136(2):528-46. Epub 2014 Jan 2.

Chemical Sciences and Engineering Division, Argonne National Laboratory , Argonne, Illinois 60439, United States.

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http://dx.doi.org/10.1021/ja408723aDOI Listing
January 2014

SCISSORS: practical considerations.

J Chem Inf Model 2014 Jan 16;54(1):5-15. Epub 2013 Dec 16.

Department of Structural Biology, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/ci400264fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207653PMC
January 2014

Calculations of the electric fields in liquid solutions.

J Phys Chem B 2013 Dec 10;117(50):16236-48. Epub 2013 Dec 10.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jp410720yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211882PMC
December 2013

Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets.

J Chem Phys 2013 Dec;139(23):234114

Department of Chemistry, Department of Structural Biology, and Department of Computer Science, Stanford University, Stanford, California 94305-5080, USA.

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http://dx.doi.org/10.1063/1.4848655DOI Listing
December 2013

Persistent topology and metastable state in conformational dynamics.

PLoS One 2013 2;8(4):e58699. Epub 2013 Apr 2.

Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058699PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614941PMC
October 2013

Probing the origins of two-state folding.

J Chem Phys 2013 Oct;139(14):145104

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.4823502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3808418PMC
October 2013

Building Markov state models with solvent dynamics.

BMC Bioinformatics 2013 21;14 Suppl 2:S8. Epub 2013 Jan 21.

Department of Computer Science, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1186/1471-2105-14-S2-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549830PMC
September 2013

Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing.

J Chem Phys 2013 Sep;139(12):121917

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.4816633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3745504PMC
September 2013

Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteins.

Methods Enzymol 2013 ;523:145-70

Department of Chemistry, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1016/B978-0-12-394292-0.00007-2DOI Listing
August 2013

Systematic improvement of a classical molecular model of water.

J Phys Chem B 2013 Aug 14;117(34):9956-72. Epub 2013 Aug 14.

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1021/jp403802cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3770532PMC
August 2013

Long Timestep Molecular Dynamics on the Graphical Processing Unit.

J Chem Theory Comput 2013 Aug;9(8):3267-3281

Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1021/ct400331rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890418PMC
August 2013

Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.

J Chem Theory Comput 2013 Jul 6;9(7):2900-6. Epub 2013 Jun 6.

Department of Chemistry, Stanford University , Stanford, California 94305-4401.

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http://dx.doi.org/10.1021/ct400132hDOI Listing
July 2013

Emergence of glass-like behavior in Markov state models of protein folding dynamics.

J Am Chem Soc 2013 Apr 3;135(15):5501-4. Epub 2013 Apr 3.

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1021/ja4002663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677858PMC
April 2013

Functional understanding of solvent structure in GroEL cavity through dipole field analysis.

J Chem Phys 2013 Apr;138(16):165101

Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.

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http://dx.doi.org/10.1063/1.4801942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651261PMC
April 2013

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.

J Chem Theory Comput 2013 Apr;9(4):2000-2009

Department of Chemistry, Stanford University, Stanford, CA, USA.

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http://pubs.acs.org/doi/10.1021/ct300878a
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http://dx.doi.org/10.1021/ct300878aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3673732PMC
April 2013

To milliseconds and beyond: challenges in the simulation of protein folding.

Curr Opin Struct Biol 2013 Feb 10;23(1):58-65. Epub 2012 Dec 10.

Department of Chemistry, Stanford University, United States.

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https://linkinghub.elsevier.com/retrieve/pii/S0959440X120018
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http://dx.doi.org/10.1016/j.sbi.2012.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3673555PMC
February 2013

Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions.

J Chem Phys 2013 Feb;138(8):085103

Department of Chemistry, Stanford University, Stanford, California 94305-4401, USA.

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http://dx.doi.org/10.1063/1.4792638DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598771PMC
February 2013