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Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin.

October 4, 2004 by Viktor

Nina Singhal, Christopher D. Snow, and Vijay S. Pande. Journal of Chemical Physics (2004) SUMMARY: How can Folding@home use thousands to millions of CPUs to efficiently simulate long timescale biomolecular…

Simulations of the role of water in the protein-folding mechanism.

October 4, 2004 by Viktor

Young Min Rhee, Eric J. Sorin, Guha Jayachandran, Erik Lindahl, & Vijay S Pande. Proceedings of the National Academy of Sciences (2004) ABSTRACT: There are many unresolved questions regarding the…

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy.

October 4, 2004 by Tor Raswill

Christopher D. Snow, Linlin Qiu, Deguo Du, Feng Gai, Stephen J. Hagen, & Vijay S Pande. Proceedings of the National Academy of Sciences (2004) ABSTRACT: We studied the microsecond folding…

Does Native State Topology Determine the RNA Folding Mechanism?

October 3, 2004 by Tor Raswill

Eric J. Sorin, Bradley J. Nakatani, Young Min Rhee, Guha Jayachandran, V Vishal, & Vijay S Pande. Journal of Molecular Biology (2004) ABSTRACT: Recent studies in protein folding suggest that…

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

October 3, 2003 by Tor Raswill

Bojan Zagrovic & Vijay S Pande. Nature Structural Biology (2003) ABSTRACT: Recently, we have proposed that, on average, the structure of the unfolded state of small, mostly alpha-helical proteins may…

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods.

October 3, 2003 by Tor Raswill

Michael R. Shirts, Eric Bair, Giles Hooker, and Vijay S Pande. Physical Review Letters (2003) ABSTRACT: We present a maximum likelihood argument for the Bennett acceptance ratio method, and derive…

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins.

October 3, 2003 by Tor Raswill

Michael R. Shirts, Jed W. Pitera, William C. Swope, and Vijay S. Pande. Journal of Chemical Physics (2003) ABSTRACT: Quantitative free energy computation involves both using a model that is…

Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin.

Simulations of the role of water in the protein-folding mechanism.

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy.

Does Native State Topology Determine the RNA Folding Mechanism?

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

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods.

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins.

Solvent Viscosity Dependence of the Folding Rate of a Small Protein: Distributed Computing Study.

https://foldingathome.org/papers/Sorin_etal_2003.pdf

Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation.