CHARMM: A program for Macromolecular Energy, Minimizations and Dynamics Calculations , B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, M. Karplus, J. Comp. Chem., 4 187 – 217 (1983).

Proc. Natl. Acad. Sci. USA

Vol. 94, pp. 10161–10166, September 1997

Biophysics

Exploring the folding free energy surface of a three-helix

bundle protein

ZHUYAN GUO*, CHARLES L. BROOKS III*†, AND ERIK M. BOCZKO‡

Detailed Analysis of Grid-Based Molecular Docking: A

Case Study of CDOCKER—A CHARMm-Based MD

Docking Algorithm

GUOSHENG WU,1 DANIEL H. ROBERTSON,1 CHARLES L. BROOKS III,2 MICHAL VIETH1

J. Comput. Chem. 24: 1549–1562, 2003

Proc. Natl. Acad. Sci. USA

Vol. 100, pp. 13916–13921, November 25, 2003

Biophysics

Exploring Flory’s isolated-pair hypothesis: Statistical mechanics of helix–coil transitions in polyalanine and the C-peptide from RNase A

Y. Zenmei Ohkubo and Charles L. Brooks III*