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Papers authored by Pande VS

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Constructing multi-resolution markov state models (msms) to elucidate RNA hairpin folding mechanisms.

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Huang X, Yao Y, Bowman GR, Sun J, Guibas LJ, Carlsson G, and Pande VS

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:228-39, 2010 - Who cited this? | PubMed ID: 19908375 | Fulltext

Multiscale dynamics of macromolecules using normal mode langevin.

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Izaguirre JA, Sweet CR, and Pande VS

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:240-51, 2010 - Who cited this? | PubMed ID: 19908376 | Fulltext

"Cross-graining": efficient multi-scale simulation via markov state models.

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Kasson PM and Pande VS

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:260-8, 2010 - Who cited this? | PubMed ID: 19908378 | Fulltext

Using generalized ensemble simulations and Markov state models to identify conformational states.

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Bowman GR, Huang X, and Pande VS

Methods (San Diego, Calif.) 49(2):197-201, 2009 Oct - Who cited this? | PubMed ID: 19410002 | Fulltext

Progress and challenges in the automated construction of Markov state models for full protein systems.

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Bowman GR, Beauchamp KA, Boxer G, and Pande VS

The Journal of chemical physics 131(12):124101, 2009 Sep 28 - Who cited this? | PubMed ID: 19791846 | Fulltext

Bayesian single-exponential kinetics in single-molecule experiments and simulations.

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Ensign DL and Pande VS

The journal of physical chemistry. B 113(36):12410-23, 2009 Sep 10 - Who cited this? | PubMed ID: 19681587 | Fulltext

Polarizable atomic multipole X-ray refinement: application to peptide crystals.

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Schnieders MJ, Fenn TD, Pande VS, and Brunger AT

Acta crystallographica. Section D, Biological crystallography 65(Pt 9):952-65, 2009 Sep - Who cited this? | PubMed ID: 19690373 | Fulltext

Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin.

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Kasson PM, Ensign DL, and Pande VS

Journal of the American Chemical Society 131(32):11338-40, 2009 Aug 19 - Who cited this? | PubMed ID: 19637916 | Fulltext

The predicted structure of the headpiece of the huntingtin protein and its implications on huntingtin aggregation.

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Kelley NW, Huang X, Tam S, Spiess C, Frydman J, and Pande VS

Journal of molecular biology 388(5):919-27, 2009 May 22 - Who cited this? | PubMed ID: 19361448 | Fulltext

Accelerating molecular dynamic simulation on graphics processing units.

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Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, Legrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS

Journal of computational chemistry 30(6):864-72, 2009 Apr 30 - Who cited this? | PubMed ID: 19191337 | Fulltext

The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations.

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Ensign DL and Pande VS

Biophysical journal 96(8):L53-5, 2009 Apr 22 - Who cited this? | PubMed ID: 19383445 | Fulltext

Topological methods for exploring low-density states in biomolecular folding pathways.

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Yao Y, Sun J, Huang X, Bowman GR, Singh G, Lesnick M, Guibas LJ, Pande VS, and Carlsson G

The Journal of chemical physics 130(14):144115, 2009 Apr 14 - Who cited this? | PubMed ID: 19368437 | Fulltext

Probing the nanosecond dynamics of a designed three-stranded Beta-sheet with a massively parallel molecular dynamics simulation.

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Voelz VA, Luttmann E, Bowman GR, and Pande VS

International journal of molecular sciences 10(3):1013-30, 2009 Mar - Who cited this? | PubMed ID: 19399235 | Fulltext

A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel.

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Voelz VA, Petrone P, and Pande VS

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:340-52, 2009 - Who cited this? | PubMed ID: 19209713 | Fulltext

Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin.

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Kasson PM and Pande VS

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:492-503, 2009 - Who cited this? | PubMed ID: 19209725 | Fulltext

Comparison of computational approaches for predicting the effects of missense mutations on p53 function.

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Chong LT, Pitera JW, Swope WC, and Pande VS

Journal of molecular graphics & modelling 27(8):978-82, 2009 - Who cited this? | PubMed ID: 19168381 | Fulltext

The roles of entropy and kinetics in structure prediction.

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Bowman GR and Pande VS

PLoS ONE 4(6):e5840, 2009 - Who cited this? | PubMed ID: 19513117 | Fulltext

Assessment of the protein-structure refinement category in CASP8.

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MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, and Dill KA

Proteins 77 Suppl 9:66-80, 2009 - Who cited this? | PubMed ID: 19714776 | Fulltext

Erratum: "Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration" [J. Chem. Phys. 122, 144107 (2005)].

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Shirts MR and Pande VS

The Journal of chemical physics 129(22):229901, 2008 Dec 14 - Who cited this? | PubMed ID: 19071951 | Fulltext

Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach.

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Kelley NW, Vishal V, Krafft GA, and Pande VS

The Journal of chemical physics 129(21):214707, 2008 Dec 7 - Who cited this? | PubMed ID: 19063575 | Fulltext

Side-chain recognition and gating in the ribosome exit tunnel.

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Petrone PM, Snow CD, Lucent D, and Pande VS

Proceedings of the National Academy of Sciences of the United States of America, 2008 Oct 22 - Who cited this? | PubMed ID: 18946046 | Fulltext

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

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Bowman GR and Pande VS

Proteins, 2008 Sep 2 - Who cited this? | PubMed ID: 18767152 | Fulltext

Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded State Ensemble.

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Bai Y, Chu VB, Lipfert J, Pande VS, Herschlag D, and Doniach S

Journal of the American Chemical Society, 2008 Aug 23 - Who cited this? | PubMed ID: 18722445 | Fulltext

A Role for Confined Water in Chaperonin Function.

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England JL, Lucent D, and Pande VS

Journal of the American Chemical Society, 2008 Aug 19 - Who cited this? | PubMed ID: 18710231 | Fulltext

Chemical Denaturants Inhibit the Onset of Dewetting.

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England JL, Pande VS, and Haran G

Journal of the American Chemical Society, 2008 Aug 16 - Who cited this? | PubMed ID: 18707183 | Fulltext

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

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Monticelli L, Sorin EJ, Tieleman DP, Pande VS, and Colombo G

Journal of computational chemistry 29(11):1740, 2008 Aug - Who cited this? | PubMed ID: 18307167 | Fulltext

Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin.

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Kasson PM and Pande VS

Biophysical journal, 2008 Jul 18 - Who cited this? | PubMed ID: 18641068 | Fulltext

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

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Luttmann E, Ensign DL, Vaidyanathan V, Houston M, Rimon N, Oland J, Jayachandran G, Friedrichs M, and Pande VS

Journal of computational chemistry, 2008 Jul 9 - Who cited this? | PubMed ID: 18615421 | Fulltext

Potential for modulation of the hydrophobic effect inside chaperonins.

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England JL and Pande VS

Biophysical journal, 2008 Jul 3 - Who cited this? | PubMed ID: 18599630 | Fulltext

Structural Insight into RNA Hairpin Folding Intermediates.

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Bowman GR, Huang X, Yao Y, Sun J, Carlsson G, Guibas LJ, and Pande VS

Journal of the American Chemical Society, 2008 Jul 1 - Who cited this? | PubMed ID: 18593120 | Fulltext

Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.

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Huang X, Bowman GR, and Pande VS

The Journal of chemical physics 128(20):205106, 2008 May 28 - Who cited this? | PubMed ID: 18513049 | Fulltext

Solvent viscosity dependence of the protein folding dynamics.

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Rhee YM and Pande VS

The journal of physical chemistry. B 112(19):6221, 2008 May 15 - Who cited this? | PubMed ID: 18229911 | Fulltext

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

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Robertson A, Luttmann E, and Pande VS

Journal of computational chemistry 29(5):694, 2008 Apr 15 - Who cited this? | PubMed ID: 17849394 | Fulltext

Normal mode partitioning of Langevin dynamics for biomolecules.

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Sweet CR, Petrone P, Pande VS, and Izaguirre JA

The Journal of chemical physics 128(14):145101, 2008 Apr 14 - Who cited this? | PubMed ID: 18412479 | Fulltext

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.

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Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, and Pande VS

Journal of medicinal chemistry 51(4):769, 2008 Feb 28 - Who cited this? | PubMed ID: 18215013 | Fulltext

Theory for an order-driven disruption of the liquid state in water.

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England JL, Park S, and Pande VS

The Journal of chemical physics 128(4):44503, 2008 Jan 28 - Who cited this? | PubMed ID: 18247965 | Fulltext

Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulations.

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Park S, Klein TE, and Pande VS

Biophysical journal 93(12):4108, 2007 Dec 15 - Who cited this? | PubMed ID: 17766343 | Fulltext

Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece.

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Ensign DL, Kasson PM, and Pande VS

Journal of molecular biology 374(3):806, 2007 Nov 30 - Who cited this? | PubMed ID: 17950314 | Fulltext

Accurate and efficient corrections for missing dispersion interactions in molecular simulations.

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Shirts MR, Mobley DL, Chodera JD, and Pande VS

The journal of physical chemistry. B 111(45):13052, 2007 Nov 15 - Who cited this? | PubMed ID: 17949030 | Fulltext

Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics.

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Kasson PM and Pande VS

PLoS computational biology 3(11), 2007 Nov - Who cited this? | PubMed ID: 18020701 | Fulltext

Persistent voids: a new structural metric for membrane fusion.

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Kasson PM, Zomorodian A, Park S, Singhal N, Guibas LJ, and Pande VS

Bioinformatics (Oxford, England) 23(14):1753, 2007 Jul 15 - Who cited this? | PubMed ID: 17488753 | Fulltext

Choosing weights for simulated tempering.

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Park S and Pande VS

Physical review. E, Statistical, nonlinear, and soft matter physics 76(1 Pt 2):16703, 2007 Jul - Who cited this? | PubMed ID: 17677590 | Fulltext

Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics.

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Hinrichs NS and Pande VS

The Journal of chemical physics 126(24):244101, 2007 Jun 28 - Who cited this? | PubMed ID: 17614531 | Fulltext

Protein folding under confinement: a role for solvent.

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Lucent D, Vishal V, and Pande VS

Proceedings of the National Academy of Sciences of the United States of America 104(25):10430, 2007 Jun 19 - Who cited this? | PubMed ID: 17563390 | Fulltext

Protein folding under confinement: a role for solvent.

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Lucent D, Vishal V, and Pande VS

Proceedings of the National Academy of Sciences of the United States of America 104(25):10430-4, 2007 Jun 19 - Who cited this? | PubMed ID: 17567207 | Fulltext

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.

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Chodera JD, Singhal N, Pande VS, Dill KA, and Swope WC

The Journal of chemical physics 126(15):155101, 2007 Apr 21 - Who cited this? | PubMed ID: 17461665 | Fulltext

Local structure formation in simulations of two small proteins.

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Jayachandran G, Vishal V, García AE, and Pande VS

Journal of structural biology 157(3):491, 2007 Mar - Who cited this? | PubMed ID: 17098444 | Fulltext

Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide.

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Kasson PM and Pande VS

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:40, 2007 - Who cited this? | PubMed ID: 17992744 | Fulltext

Bayesian update method for adaptive weighted sampling.

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Park S, Ensign DL, and Pande VS

Physical review. E, Statistical, nonlinear, and soft matter physics 74(6 Pt 2):66703, 2006 Dec - Who cited this? | PubMed ID: 17280173 | Fulltext

Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles.

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Zagrovic B and Pande VS

Journal of the American Chemical Society 128(36):11742, 2006 Sep 13 - Who cited this? | PubMed ID: 16953598 | Fulltext

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