Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 26, Issue 16, Pages 1752-1780Publisher
WILEY-BLACKWELL
DOI: 10.1002/jcc.20292
Keywords
IMPACT; Monte Carlo simulation; QM/MM applications
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Funding
- NIGMS NIH HHS [R01 GM043340, R01 GM030580, GM52018, R01 GM052018, GM30580, R01 GM040526, R01 GM052018-12, GM40526, GM43340] Funding Source: Medline
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We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its cur-rent 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. (c) 2005 Wiley Periodicals, Inc.
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