1. All-atom empirical potential for molecular modeling and dynamics studies of proteins
- Author
-
MacKerell, A.D., Jr., Bashford, D., Bellott, M., Dunbrack, R.L., Jr., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E., III, Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, j., Watanabe, M., Wiorkiewicz-Kuczera, j., Karplus, M., and Yin, D.
- Subjects
Proteins -- Research ,Molecular dynamics -- Research ,Molecules -- Analysis ,Chemicals, plastics and rubber industries - Abstract
A study was conducted to develop novel protein parameters for the all-atom empirical energy function in the CHARMM program. The parameter evaluation focused on a self-consistent approach designed to realize a balance between the internal and interaction terms of the force field and interactions associated with solvents and solutes. The parameters were then obtained by fitting an extended set of experimental and ab initio results. In addition, internal parametrizations were selected to duplicate geometries from crystal structures, Raman spectroscopic data and ab initio computations.
- Published
- 1998