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Integrated Modeling Program, Applied Chemical Theory (IMPACT)
Journal of computational chemistry, 2005-12, Vol.26 (16), p.1752-1780
Banks, Jay L.
Beard, Hege S.
Cao, Yixiang
Cho, Art E.
Damm, Wolfgang
Farid, Ramy
Felts, Anthony K.
Halgren, Thomas A.
Mainz, Daniel T.
Maple, Jon R.
Murphy, Robert
Philipp, Dean M.
Repasky, Matthew P.
Zhang, Linda Y.
Berne, Bruce J.
Friesner, Richard A.
Gallicchio, Emilio
Levy, Ronald M.
2005
Volltextzugriff (PDF)
Details
Autor(en) / Beteiligte
Banks, Jay L.
Beard, Hege S.
Cao, Yixiang
Cho, Art E.
Damm, Wolfgang
Farid, Ramy
Felts, Anthony K.
Halgren, Thomas A.
Mainz, Daniel T.
Maple, Jon R.
Murphy, Robert
Philipp, Dean M.
Repasky, Matthew P.
Zhang, Linda Y.
Berne, Bruce J.
Friesner, Richard A.
Gallicchio, Emilio
Levy, Ronald M.
Titel
Integrated Modeling Program, Applied Chemical Theory (IMPACT)
Ist Teil von
Journal of computational chemistry, 2005-12, Vol.26 (16), p.1752-1780
Ort / Verlag
Hoboken: Wiley Subscription Services, Inc., A Wiley Company
Erscheinungsjahr
2005
Quelle
MEDLINE
Beschreibungen/Notizen
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. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1752–1780, 2005
Sprache
Englisch
Identifikatoren
ISSN: 0192-8651
eISSN: 1096-987X
DOI: 10.1002/jcc.20292
Titel-ID: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2742605
Format
–
Schlagworte
Chemistry
,
Computer based modeling
,
Computer Simulation
,
Drug Design
,
IMPACT
,
Models, Chemical
,
Models, Molecular
,
Molecules
,
Monte Carlo Method
,
Monte Carlo simulation
,
Protein Structure, Tertiary
,
QM/MM applications
,
Quantum Theory
,
Software
,
Solvents - chemistry
,
Thermodynamics
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