Predicting small-molecule solvation free energies: A blind challenge test for computational chemistry

Anthony Nicholls, David L. Mobley, J. Peter Guthrie, John D. Chodera, and Vijay S. Pande.
J. Med. Chem. 51:769, 2008. [DOI] [PDF]

A blind evaluation of the accuracy of alchemical free energy methods for computing gas-to-water transfer free energies (solvation free energies) of small molecules demonstrates that modern forcefields are likely sufficiently accurate to be useful in drug design.

Treating entropy and conformational changes in implicit solvent simulations of small molecules

David L. Mobley, John D. Chodera, and Ken A. Dill
J. Phys. Chem. B 112:938, 2008. [DOI] [PDF]

A quantitative examination of how much conformational entropy contributes to hydration free energies of small molecules, with implications for ligand binding.

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

Michael R. Shirts, David L. Mobley, John D. Chodera, and Vijay S. Pande.  
J. Phys. Chem. B 111:13052, 2007. [DOI] [PDF]

We identify a major source of systematic error in absolute alchemical free energy calculations of ligand binding and show how a simple procedure can inexpensively and accurately eliminate it.

Protein Folding by Zipping and Assembly

S. Banu Ozkan, G. Albert Wu, John D. Chodera, and Ken A. Dill.
Proc. Natl. Acad. Sci. USA 104:11987, 2007. [DOI] [PDF]

A review of the utility of the proposed zipping and assembly mechanism for the concomitant formation of secondary and tertiary structure in protein folding for predicting folding pathways and native structures.

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

John D. Chodera*, Nina Singhal*, William C. Swope, Jed W. Pitera, Vijay S. Pande, and Ken A. Dill.
J. Chem. Phys. 126:155101, 2007. [DOI] [PDF]

Proposing one of the first automated algorithms for discovering kinetically metastable states of biomolecules from molecular simulations, this paper shows how many biomolecules can possess numerous distinct long-lived conformational states even though the the equilibrium populations of these states may too small for standard structural biology techniques to detect.

Long-time protein folding dynamics from short-time molecular dynamics simulations

John D. Chodera, William C. Swope, Jed W. Pitera, and Ken A. Dill.
Multiscale Model. Simul. 5:1214, 2006. [DOI] [PDF]

We show how the long-time dynamics of biomolecular systems can be recapitulated from statistics collected from short molecular simulations sampling transitions between kinetically metastable states.