Papers

pande-labs-pubs

RSS feed from PubMed for the latest 100 Pande Lab publications.

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 VS 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 L, Shukla 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 KA, Voelz 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 DE, 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, Ren 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 VS 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...
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 VS 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. 2011 Sep 7; 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, Langan 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...
Simple theory of protein folding kinetics.
Phys Rev Lett. 2010 Nov 5;105(19):198101 Authors: Pande VS more...
Atomistic folding simulations of the five-helix bundle protein λ(6−85).
J Am Chem Soc. 2011 Feb 2;133(4):664-7 Authors: Bowman GR, Voelz VA, Pande VS more...
Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation.
J Phys Chem B. 2011 Jan 20;115(2):319-28 Authors: Stumpe MC, Blinov N, Wishart D, more...
Taming the complexity of protein folding.
Curr Opin Struct Biol. 2011 Feb;21(1):4-11 Authors: Bowman GR, Voelz VA, Pande VS more...
Non-bulk-like solvent behavior in the ribosome exit tunnel.
PLoS Comput Biol. 2010;6(10):e1000963 Authors: Lucent D, Snow CD, Aitken CE, Pande VS more...
Bayesian inference for Brownian dynamics.
Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jul;82(1 Pt 2):016705 Authors: Ensign DL, Pande more...
Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails.
PLoS Comput Biol. 2010 Jun;6(6):e1000829 Authors: Kasson PM, Lindahl E, Pande VS more...
Everything you wanted to know about Markov State Models but were afraid to ask.
Methods. 2010 Sep;52(1):99-105 Authors: Pande VS, Beauchamp K, Bowman GR more...
CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations.
J Chem Theory Comput. 2010 Feb 9;6(2):434-437 Authors: Eastman P, Pande VS more...
Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules.
Biophys J. 2010 Jun 16;98(12):2984-92 Authors: Fenn TD, Schnieders MJ, Brunger AT, Pande VS more...
Protein folded states are kinetic hubs.
Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10890-5 Authors: Bowman GR, Pande more...
SCISSORS: a linear-algebraical technique to rapidly approximate chemical similarities.
J Chem Inf Model. 2010 Jun 28;50(6):1075-88 Authors: Haque IS, Pande VS more...
Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework.
Biochem Cell Biol. 2010 Apr;88(2):359-69 Authors: England JL, Pande VS more...
Network models for molecular kinetics and their initial applications to human health.
Cell Res. 2010 Jun;20(6):622-30 Authors: Bowman GR, Huang X, Pande VS more...
Unfolded-state dynamics and structure of protein L characterized by simulation and experiment.
J Am Chem Soc. 2010 Apr 7;132(13):4702-9 Authors: Voelz VA, Singh VR, Wedemeyer WJ, more...
SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUs.
J Chem Inf Model. 2010 Apr 26;50(4):560-4 Authors: Haque IS, Pande VS, Walters WP more...
Current status of the AMOEBA polarizable force field.
J Phys Chem B. 2010 Mar 4;114(8):2549-64 Authors: Ponder JW, Wu C, Ren P, more...
Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39).
J Am Chem Soc. 2010 Feb 10;132(5):1526-8 Authors: Voelz VA, Bowman GR, Beauchamp K, more...
Enhanced modeling via network theory: Adaptive sampling of Markov state models.
J Chem Theory Comput. 2010;6(3):787-794 Authors: Bowman GR, Ensign DL, Pande VS more...
Bayesian detection of intensity changes in single molecule and molecular dynamics trajectories.
J Phys Chem B. 2010 Jan 14;114(1):280-92 Authors: Ensign DL, Pande VS more...
"Cross-graining": efficient multi-scale simulation via Markov state models.
"Cross-graining": efficient multi-scale simulation via Markov state models. Pac Symp Biocomput. 2010;:260-8 Authors: Kasson PM, Pande more...
Multiscale dynamics of macromolecules using normal mode Langevin.
Pac Symp Biocomput. 2010;:240-51 Authors: Izaguirre JA, Sweet CR, Pande VS more...
Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms.
Pac Symp Biocomput. 2010;:228-39 Authors: Huang X, Yao Y, Bowman GR, Sun J, Guibas LJ, more...
Do conformational biases of simple helical junctions influence RNA folding stability and specificity?
RNA. 2009 Dec;15(12):2195-205 Authors: Chu VB, Lipfert J, Bai Y, Pande VS, Doniach S, more...
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.
J Comput Chem. 2010 Apr 30;31(6):1268-72 Authors: Eastman P, Pande VS more...
Rapid equilibrium sampling initiated from nonequilibrium data.
Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19765-9 Authors: Huang X, Bowman more...
Progress and challenges in the automated construction of Markov state models for full protein systems.
J Chem Phys. 2009 Sep 28;131(12):124101 Authors: Bowman GR, Beauchamp KA, Boxer G, Pande more...
Assessment of the protein-structure refinement category in CASP8.
Proteins. 2009;77 Suppl 9:66-80 Authors: MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson more...
Polarizable atomic multipole X-ray refinement: application to peptide crystals.
Acta Crystallogr D Biol Crystallogr. 2009 Sep;65(Pt 9):952-65 Authors: Schnieders MJ, Fenn TD, Pande more...
Bayesian single-exponential kinetics in single-molecule experiments and simulations.
J Phys Chem B. 2009 Sep 10;113(36):12410-23 Authors: Ensign DL, Pande VS more...
Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin.
J Am Chem Soc. 2009 Aug 19;131(32):11338-40 Authors: Kasson PM, Ensign DL, Pande VS more...
The roles of entropy and kinetics in structure prediction.
PLoS One. 2009;4(6):e5840 Authors: Bowman GR, Pande VS more...
PAPER--accelerating parallel evaluations of ROCS.
J Comput Chem. 2010 Jan 15;31(1):117-32 Authors: Haque IS, Pande VS more...
Using generalized ensemble simulations and Markov state models to identify conformational states.
Methods. 2009 Oct;49(2):197-201 Authors: Bowman GR, Huang X, Pande VS more...
Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation.
Int J Mol Sci. 2009 Mar;10(3):1013-30 Authors: Voelz VA, Luttmann E, Bowman GR, Pande VS more...