Publication： Journal of Computational Chemistry

Date of Publication: 24 April 2005

Authors： JAY L. BANKS, HEGE S. BEARD, YIXIANG CAO, ART E. CHO, WOLFGANG DAMM, RAMY FARID, ANTHONY K. FELTS, THOMAS A. HALGREN, DANIEL T. MAINZ, JON R. MAPLE, ROBERT MURPHY, DEAN M. PHILIPP, MATTHEW P. REPASKY, LINDA Y. ZHANG, BRUCE J. BERNE, RICHARD A. FRIESNER, EMILIO GALLICCHIO, RONALD M. LEVY

DOI 10.1002/jcc.20292

We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when used together with new atom typing and parameter assignment modules, have greatly expanded the coverage of organic compounds and medicinally relevant ligands. As we discuss in this review, explicit solvent simulations have been used to guide our design of implicit solvent models based on the generalized Born framework and a novel nonpolar estimator that have recently been incorporated into the program. With IMPACT it is possible to use several different advanced conformational sampling algorithms based on combining features of molecular dynamics and Monte Carlo simulations. The program includes two specialized molecular mechanics modules: Glide, a high-throughput docking program, and QSite, a mixed quantum mechanics/molecular mechanics module. These modules employ the IMPACT infrastructure as a starting point for the construction of the protein model and assignment of molecular mechanics parameters, but have then been developed to meet specialized objectives with respect to sampling and the energy function.