Papers

pande-labs-pubs

RSS feed from PubMed for the latest Pande Lab publications.

Advanced Potential Energy Surfaces for Molecular Simulation.
J Phys Chem B. 2016 Aug 11; Authors: Albaugh A, Boateng HA, Bradshaw RT, Demerdash more...
Corrigendum: Conformational heterogeneity of the calmodulin binding interface.
Nat Commun. 2016;7:12318 Authors: Shukla D, Peck A, Pande VS more...
Transition path theory analysis of c-Src kinase activation.
Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9193-8 Authors: Meng Y, Shukla D, more...
Finding Our Way in the Dark Proteome.
J Am Chem Soc. 2016 Aug 10;138(31):9730-42 Authors: Bhowmick A, Brookes DH, Yost SR, Dyson more...
Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase.
J Mol Biol. 2016 Jul 3;428(13):2758-68 Authors: Peck A, Sunden F, Andrews LD, Pande VS, more...
Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.
Biophys J. 2016 Apr 26;110(8):1716-9 Authors: Schwantes CR, Shukla D, Pande VS more...
Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models.
Nat Chem. 2016 May;8(5):419-25 Authors: Dodani SC, Kiss G, Cahn JK, Su Y, Pande VS, more...
Conformational heterogeneity of the calmodulin binding interface.
Nat Commun. 2016;7:10910 Authors: Shukla D, Peck A, Pande VS more...
Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations.
Nat Genet. 2016 Feb;48(2):117-25 Authors: Araya CL, Cenik C, Reuter JA, Kiss G, Pande more...
Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways.
J Chem Theory Comput. 2016 Feb 9;12(2):638-49 Authors: Wang LP, McGibbon RT, Pande VS, Martinez TJ more...
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
J Chem Theory Comput. 2016 Jan 12;12(1):405-13 Authors: Lee J, Cheng X, Swails JM, more...
Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics.
J Chem Theory Comput. 2015 Mar 10;11(3):1094-101 Authors: Harrigan MP, Shukla D, Pande VS more...
Potential-based dynamical reweighting for Markov state models of protein dynamics.
J Chem Theory Comput. 2015 Jun 9;11(6):2412-20 Authors: Weber JK, Pande VS more...
Modeling molecular kinetics with tICA and the kernel trick.
J Chem Theory Comput. 2015 Feb 10;11(2):600-8 Authors: Schwantes CR, Pande VS more...
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.
Biophys J. 2015 Oct 20;109(8):1528-32 Authors: McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails more...
Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.
Nat Chem. 2015 Sep;7(9):759 Authors: Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, more...
Heat dissipation guides activation in signaling proteins.
Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10377-82 Authors: Weber JK, Shukla more...
Efficient maximum likelihood parameterization of continuous-time Markov processes.
J Chem Phys. 2015 Jul 21;143(3):034109 Authors: McGibbon RT, Pande VS more...
United polarizable multipole water model for molecular mechanics simulation.
J Chem Phys. 2015 Jul 7;143(1):014504 Authors: Qi R, Wang LP, Wang Q, Pande more...
OpenMM: A Hardware Independent Framework for Molecular Simulations.
Comput Sci Eng. 2015 Jul 1;12(4):34-39 Authors: Eastman P, Pande VS more...
Free energy landscape of activation in a signalling protein at atomic resolution.
Nat Commun. 2015;6:7284 Authors: Pontiggia F, Pachov DV, Clarkson MW, Villali J, Hagan MF, more...
A network of molecular switches controls the activation of the two-component response regulator NtrC.
Nat Commun. 2015;6:7283 Authors: Vanatta DK, Shukla D, Lawrenz M, Pande VS more...
Percolation-like phase transitions in network models of protein dynamics.
J Chem Phys. 2015 Jun 7;142(21):215105 Authors: Weber JK, Pande VS more...
Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches.
Methods Enzymol. 2015;557:551-72 Authors: Shukla D, Lawrenz M, Pande VS more...
Entropy-production-driven oscillators in simple nonequilibrium networks.
Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Mar;91(3):032136 Authors: Weber JK, Pande VS more...
Variational cross-validation of slow dynamical modes in molecular kinetics.
J Chem Phys. 2015 Mar 28;142(12):124105 Authors: McGibbon RT, Pande VS more...
The dynamic conformational cycle of the group I chaperonin C-termini revealed via molecular dynamics simulation.
PLoS One. 2015;10(3):e0117724 Authors: Dalton KM, Frydman J, Pande VS more...
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.
J Phys Chem B. 2015 Jul 23;119(29):9423-37 Authors: Laury ML, Wang LP, Pande VS, more...
Markov state models provide insights into dynamic modulation of protein function.
Acc Chem Res. 2015 Feb 17;48(2):414-22 Authors: Shukla D, Hernández CX, Weber JK, more...
Cloud computing approaches for prediction of ligand binding poses and pathways.
Sci Rep. 2015;5:7918 Authors: Lawrenz M, Shukla D, Pande VS more...
Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations.
J Chem Theory Comput. 2014 Dec 9;10(12):5217-5223 Authors: Sultan MM, Kiss G, Shukla D, Pande more...
Discovering chemistry with an ab initio nanoreactor.
Nat Chem. 2014 Dec;6(12):1044-8 Authors: Wang LP, Titov A, McGibbon R, Liu F, Pande more...
Perspective: Markov models for long-timescale biomolecular dynamics.
J Chem Phys. 2014 Sep 7;141(9):090901 Authors: Schwantes CR, McGibbon RT, Pande VS more...
Dynamical phase transitions reveal amyloid-like states on protein folding landscapes.
Biophys J. 2014 Aug 19;107(4):974-82 Authors: Weber JK, Jack RL, Schwantes CR, Pande more...
Complex pathways in folding of protein G explored by simulation and experiment.
Biophys J. 2014 Aug 19;107(4):947-55 Authors: Lapidus LJ, Acharya S, Schwantes CR, Wu more...
Building Force Fields: An Automatic, Systematic, and Reproducible Approach.
J Phys Chem Lett. 2014 Jun 5;5(11):1885-91 Authors: Wang LP, Martinez TJ, Pande VS more...
Statistical model selection for Markov models of biomolecular dynamics.
J Phys Chem B. 2014 Jun 19;118(24):6475-81 Authors: McGibbon RT, Schwantes CR, Pande VS more...
Bayesian energy landscape tilting: towards concordant models of molecular ensembles.
Biophys J. 2014 Mar 18;106(6):1381-90 Authors: Beauchamp KA, Pande VS, Das R more...
A molecular interpretation of 2D IR protein folding experiments with Markov state models.
Biophys J. 2014 Mar 18;106(6):1359-70 Authors: Baiz CR, Lin YS, Peng CS, Beauchamp more...
Activation pathway of Src kinase reveals intermediate states as targets for drug design.
Nat Commun. 2014;5:3397 Authors: Shukla D, Meng Y, Roux B, Pande VS more...
Long Timestep Molecular Dynamics on the Graphical Processing Unit.
J Chem Theory Comput. 2013 Aug 13;9(8):3267-3281 Authors: Sweet JC, Nowling RJ, Cickovski T, Sweet more...
Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets.
J Chem Phys. 2013 Dec 21;139(23):234114 Authors: Wagoner JA, Pande VS more...
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.
Nat Chem. 2014 Jan;6(1):15-21 Authors: Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding more...
Inferring the rate-length law of protein folding.
PLoS One. 2013;8(12):e78606 Authors: Lane TJ, Pande VS more...
Calculations of the electric fields in liquid solutions.
J Phys Chem B. 2013 Dec 19;117(50):16236-48 Authors: Fried SD, Wang LP, Boxer SG, more...
Understanding protein folding using Markov state models.
Adv Exp Med Biol. 2014;797:101-6 Authors: Pande VS more...
Introduction and overview of this book.
Adv Exp Med Biol. 2014;797:1-6 Authors: Bowman GR, Pande VS, Noé F more...
SCISSORS: practical considerations.
J Chem Inf Model. 2014 Jan 27;54(1):5-15 Authors: Kearnes SM, Haque IS, Pande VS more...
Chemical kinetics and mechanisms of complex systems: a perspective on recent theoretical advances.
J Am Chem Soc. 2014 Jan 15;136(2):528-46 Authors: Klippenstein SJ, Pande VS, Truhlar DG more...
SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discovery.
PLoS One. 2013;8(11):e79568 Authors: Novick PA, Ortiz OF, Poelman J, Abdulhay AY, Pande VS more...
Probing the origins of two-state folding.
J Chem Phys. 2013 Oct 14;139(14):145104 Authors: Lane TJ, Schwantes CR, Beauchamp KA, Pande more...
Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing.
J Chem Phys. 2013 Sep 28;139(12):121917 Authors: Weber JK, Pande VS more...
Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.
J Chem Theory Comput. 2013 Jul 9;9(7):2900-6 Authors: McGibbon RT, Pande VS more...
Systematic improvement of a classical molecular model of water.
J Phys Chem B. 2013 Aug 29;117(34):9956-72 Authors: Wang LP, Head-Gordon T, Ponder JW, more...
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.
J Chem Theory Comput. 2013 Apr 9;9(4):2000-2009 Authors: Schwantes CR, Pande VS more...
Functional understanding of solvent structure in GroEL cavity through dipole field analysis.
J Chem Phys. 2013 Apr 28;138(16):165101 Authors: Weber JK, Pande VS more...
Persistent topology and metastable state in conformational dynamics.
PLoS One. 2013;8(4):e58699 Authors: Chang HW, Bacallado S, Pande VS, Carlsson GE more...
Emergence of glass-like behavior in Markov state models of protein folding dynamics.
J Am Chem Soc. 2013 Apr 17;135(15):5501-4 Authors: Weber JK, Jack RL, Pande VS more...
Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions.
J Chem Phys. 2013 Feb 28;138(8):085103 Authors: Weber JK, Pande VS more...
Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteins.
Methods Enzymol. 2013;523:145-70 Authors: Kiss G, Pande VS, Houk KN more...
Building Markov state models with solvent dynamics.
BMC Bioinformatics. 2013;14 Suppl 2:S8 Authors: Gu C, Chang HW, Maibaum L, Pande VS, more...
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.
J Chem Theory Comput. 2013 Jan 8;9(1):461-469 Authors: Eastman P, Friedrichs MS, Chodera JD, Radmer more...
Effects of familial mutations on the monomer structure of Aβ₄₂.
Biophys J. 2012 Dec 19;103(12):L47-9 Authors: Lin YS, Pande VS more...
To milliseconds and beyond: challenges in the simulation of protein folding.
Curr Opin Struct Biol. 2013 Feb;23(1):58-65 Authors: Lane TJ, Shukla D, Beauchamp KA, Pande more...
Eigenvalues of the homogeneous finite linear one step master equation: applications to downhill folding.
J Chem Phys. 2012 Dec 7;137(21):215106 Authors: Lane TJ, Pande VS more...
Reducing the effect of Metropolization on mixing times in molecular dynamics simulations.
J Chem Phys. 2012 Dec 7;137(21):214105 Authors: Wagoner JA, Pande VS more...
Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.
Nat Immunol. 2012 Dec;13(12):1187-95 Authors: Ring AM, Lin JX, Feng D, Mitra S, Rickert more...
Marked difference in saxitoxin and tetrodotoxin affinity for the human nociceptive voltage-gated sodium channel (Nav1.7) [corrected].
Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):18102-7 Authors: Walker JR, Novick more...
Simple few-state models reveal hidden complexity in protein folding.
Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17807-13 Authors: Beauchamp KA, McGibbon more...
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.
J Chem Theory Comput. 2012 Apr 10;8(4):1409-1414 Authors: Beauchamp KA, Lin YS, Das R, Pande more...
Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment.
J Am Chem Soc. 2012 Aug 1;134(30):12565-77 Authors: Voelz VA, Jäger M, Yao S, more...
Precursor directed biosynthesis of an orthogonally functional erythromycin analogue: selectivity in the ribosome macrolide binding pocket.
J Am Chem Soc. 2012 Jul 25;134(29):12259-65 Authors: Harvey CJ, Puglisi JD, Pande VS, more...
A simple model predicts experimental folding rates and a hub-like topology.
J Phys Chem B. 2012 Jun 14;116(23):6764-74 Authors: Lane TJ, Pande VS more...
Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'.
Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'. Nature. 2012 Apr 26;484(7395):529-33 Authors: more...
Design of β-amyloid aggregation inhibitors from a predicted structural motif.
J Med Chem. 2012 Apr 12;55(7):3002-10 Authors: Novick PA, Lopes DH, Branson KM, Esteras-Chopo more...
Protein folding is mechanistically robust.
Biophys J. 2012 Feb 22;102(4):859-67 Authors: Weber JK, Pande VS more...
Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer.
Biophys J. 2012 Jan 18;102(2):315-24 Authors: Lin YS, Bowman GR, Beauchamp KA, Pande more...
Sequence coevolution between RNA and protein characterized by mutual information between residue triplets.
PLoS One. 2012;7(1):e30022 Authors: Brandman R, Brandman Y, Pande VS more...
A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosome.
PLoS One. 2012;7(1):e29377 Authors: Brandman R, Brandman Y, Pande VS more...
Characterization and rapid sampling of protein folding Markov state model topologies.
J Chem Theory Comput. 2011 Oct 11;7(10):3405-3411 Authors: Weber JK, Pande VS more...
MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale.
J Chem Theory Comput. 2011 Oct 11;7(10):3412-3419 Authors: Beauchamp KA, Bowman GR, Lane TJ, Maibaum more...
Calculation of rate spectra from noisy time series data.
Proteins. 2012 Feb;80(2):342-51 Authors: Voelz VA, Pande VS more...
Simbios: an NIH national center for physics-based simulation of biological structures.
J Am Med Inform Assoc. 2012 Mar-Apr;19(2):186-9 Authors: Delp SL, Ku JP, Pande VS, more...
Markov state model reveals folding and functional dynamics in ultra-long MD trajectories.
J Am Chem Soc. 2011 Nov 16;133(45):18413-9 Authors: Lane TJ, Bowman GR, Beauchamp K, more...
Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments.
Phys Rev Lett. 2011 Aug 26;107(9):098102 Authors: Chodera JD, Pande VS more...
(Compressed) sensing and sensibility.
Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):14713-4 Authors: Pande VS more...
Anatomy of high-performance 2D similarity calculations.
J Chem Inf Model. 2011 Sep 26;51(9):2345-51 Authors: Haque IS, Pande VS, Walters WP more...
Error bounds on the SCISSORS approximation method.
J Chem Inf Model. 2011 Sep 26;51(9):2248-53 Authors: Haque IS, Pande VS more...
The social network (of protein conformations).
Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):12969-70 Authors: Chodera JD, Pande more...
Rationally designed turn promoting mutation in the amyloid-β peptide sequence stabilizes oligomers in solution.
PLoS One. 2011;6(7):e21776 Authors: Rajadas J, Liu CW, Novick P, Kelley NW, Inayathullah M, more...
Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments.
Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12734-9 Authors: Beauchamp KA, Ensign more...
Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.
J Chem Phys. 2011 Jun 28;134(24):244108 Authors: Prinz JH, Chodera JD, Pande VS, Swope more...
Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.
J Chem Phys. 2011 Jun 28;134(24):244107 Authors: Chodera JD, Swope WC, Noé F, Prinz more...
CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.
Bioinformatics. 2011 Aug 15;27(16):2322-3 Authors: Kohlhoff KJ, Sosnick MH, Hsu WT, Pande VS, Altman more...
A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent.
J Chem Phys. 2011 Jun 7;134(21):214103 Authors: Wagoner JA, Pande VS more...
Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.
Structure. 2011 Apr 13;19(4):523-33 Authors: Fenn TD, Schnieders MJ, Mustyakimov M, Wu C, more...
Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals.
J Chem Theory Comput. 2011 Apr 12;7(4):1141-56 Authors: Schnieders MJ, Fenn TD, Pande VS more...
A bundling of viral fusion mechanisms.
Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3827-8 Authors: Kasson PM, Pande more...
Water ordering at membrane interfaces controls fusion dynamics.
J Am Chem Soc. 2011 Mar 23;133(11):3812-5 Authors: Kasson PM, Lindahl E, Pande VS more...
Alchemical free energy methods for drug discovery: progress and challenges.
Curr Opin Struct Biol. 2011 Apr;21(2):150-60 Authors: Chodera JD, Mobley DL, Shirts MR, Dixon more...