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.

Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent

David L. Mobley, Élise Dumont, John D. Chodera, Christopher I. Bayly, Matthew D. Cooper, and Ken A. Dill.
J. Phys. Chem. B 111:2242, 2007. [DOI] [PDF]

We compare a number of popular methods for deriving charge models for small molecules, deriving lessons about best practices for accurate simulations.

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.

Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations

John D. Chodera, William C. Swope, Jed W. Pitera, Chaok Seok, and Ken A. Dill.
J. Chem. Theor. Comput. 3(1):26–41, 2007 [DOI] [PDF]

The weighted histogram analysis method (WHAM), a mainstay of molecular dynamics simulation analysis, is thoroughly explained and modernized for the analysis of simulated and parallel tempering simulation data. 

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

David L. Mobley, John D. Chodera, and Ken A. Dill.
J. Chem. Phys. 125:084902, 2006. [DOI] [PDF]

We illustrate how orientational restraints can be used to greatly reduce the computational effort in alchemical calculations of ligand binding free energies, and clarify how symmetry corrections are necessary when molecules contain symmetric or pseudosymmetric substituents.

MOPED: Method for optimizing physical energy parameters using decoys

Chaok Seok, J. B. Rosen, John D. Chodera, and Ken A. Dill. 
J. Comput. Chem., 24(1):89-97 (2003) [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. 

An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase

Tai-Sung Lee*, Lillian T. Chong*, John D. Chodera, and Peter A. Kollman. 
* These authors contributed equally to the work. 
J. Am. Chem. Soc., 123 (51):12837-12848 (2001) [DOI] [PDF]

A combined QM and MD analysis of potential plausible mechanisms to explain the enormous catalytic acceleration of one of the most proficient enzymes known.