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.