A simple method for automated equilibration detection in molecular simulations

Por Chodera, John D.
Publicado no J Chem Theory Comput (2016)

The social network (of protein conformations)

Por Chodera, John D., Pande, Vijay S.
Publicado em 2011

Markov state models of biomolecular conformational dynamics

Por Chodera, John D., Noé, Frank
Publicado em 2014

Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments

Por Chodera, John D., Pande, Vijay S.
Publicado no Phys Rev Lett (2011)

Statistically optimal analysis of samples from multiple equilibrium states

Por Shirts, Michael R., Chodera, John D.
Publicado em 2008

Entropy-enthalpy compensation: Role and ramifications in biomolecular ligand recognition and design

Por Chodera, John D., Mobley, David L.
Publicado em 2013

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

Por Bacallado, Sergio, Chodera, John D., Pande, Vijay
Publicado em 2009

Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages

Por Minh, David D. L., Chodera, John D.
Publicado em 2009

Spectral Rate Theory for Two-State Kinetics

Por Prinz, Jan-Hendrik, Chodera, John D., Noé, Frank
Publicado em 2014

Modeling error in experimental assays using the bootstrap principle: Understanding discrepancies between assays using different dispensing technologies

Por Hanson, Sonya M., Ekins, Sean, Chodera, John D.
Publicado no J Comput Aided Mol Des (2015)

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

Por Mobley, David L., Chodera, John D., Dill, Ken A.
Publicado em 2007

Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules

Por Mobley, David L., Dill, Ken A., Chodera, John D.
Publicado em 2008

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

Por Mobley, David L., Chodera, John D., Dill, Ken A.
Publicado em 2006

Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems

Por Sivak, David A., Chodera, John D., Crooks, Gavin E.
Publicado em 2014

The molten globule state is unusually deformable under mechanical force

Por Elms, Phillip J., Chodera, John D., Bustamante, Carlos, Marqusee, Susan
Publicado em 2012

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

Por Wang, Kai, Yang, Yanzhi, Chodera, John D., Shirts, Michael R.
Publicado em 2013

Protein folding by zipping and assembly

Por Ozkan, S. Banu, Wu, G. Albert, Chodera, John D., Dill, Ken A.
Publicado em 2007

Limitations of Constant-Force-Feedback Experiments

Por Elms, Phillip J., Chodera, John D., Bustamante, Carlos J., Marqusee, Susan
Publicado em 2012

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

Por Nilmeier, Jerome P., Crooks, Gavin E., Minh, David D. L., Chodera, John D.
Publicado em 2011

The Ribosome Modulates Nascent Protein Folding

Por Kaiser, Christian M., Goldman, Daniel H., Chodera, John D., Tinoco, Ignacio, Bustamante, Carlos
Publicado em 2011