Efficient Numerical Reconstruction of Protein Folding Kinetics with Partial Path Sampling and Pathlike Variables

Unknown

(2018)   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Unknown

(2016)   JOURNAL OF COMPUTATIONAL CHEMISTRY

Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations

(2011) Weihua Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protonation/deprotonation effects on the stability of the Trp-cage miniprotein

(2011) Camilo A. Jimenez-Cruz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Kinetics and mechanism of the unfolding native-to-loop transition of Trp-cage in explicit solvent via optimized forward flux sampling simulations

(2010) Camilo Velez-Vega et al.   JOURNAL OF CHEMICAL PHYSICS

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein

(2010) Ryan Day et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems

(2009) David R. Glowacki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

(2008) Jarek Juraszek et al.   BIOPHYSICAL JOURNAL

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation