Markov state models of biomolecular conformational dynamics

John D. Chodera and Frank Noé.
Curr. Opin. Struct. Biol., 25:135-144, 2014. [DOI] [PDF]

A review of the exciting developments in the stochastic modeling of biomolecular dynamics over the last few years.

Entropy-enthalpy compensation: Role and ramifications for rational ligand design

John D. Chodera and David L. Mobley.
Annu. Rev. Biophys. 42:121, 2013. [DOI] [PDF]

Entropy-enthalpy compensation is likely a universal phenomena, but not as severe as widely thought, and likely not of enormous concern for drug discovery and ligand design.

Markov models of molecular kinetics: Generation and validation

Jan-Hendrik Prinz, Hao Wu, Marco Sarich, Bettina Keller, Martin Fischbach, Martin Held, John D. Chodera, Christof Schüttle, and Frank Noé.
J. Chem. Phys. 134:174105, 2011. [DOI] [PDF]

A review of current best practices for the generation and validation of Markov state models for describing the stochastic dynamics of biomolecular systems.

Free energy methods in drug discovery and design: Progress and challenges

John D. Chodera, David L. Mobley, Michael R. Shirts, Richard W. Dixon, Kim M. Branson, and Vijay S. Pande.
Curr. Opin. Struct. Biol. 21:150, 2011. [DOI] [PDF]

A review of the opportunities and challenges for alchemical free energy calculations in drug discovery and design.

The protein folding problem: When will it be solved?

Ken A. Dill, S. Banu Ozkan, Thomas R. Weikl, John D. Chodera, and Vincent A. Voelz.
Curr. Opin. Struct. Biol. 17:342, 2007. [DOI] [PDF]

A review of the current state of the protein folding problem.