Empirical force fields for biological macromolecules: overview and issues.

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TitleEmpirical force fields for biological macromolecules: overview and issues.
Publication TypeJournal Article
Year of Publication2004
AuthorsMackerell, AD
JournalJ Comput Chem
Volume25
Issue13
Pagination1584-604
Date Published2004 Oct
ISSN0192-8651
KeywordsAlgorithms, Carbohydrates, Computer Simulation, Lipids, Macromolecular Substances, Models, Molecular, Nucleic Acids, Proteins, Static Electricity, Structure-Activity Relationship, Thermodynamics
Abstract

Empirical force field-based studies of biological macromolecules are becoming a common tool for investigating their structure-activity relationships at an atomic level of detail. Such studies facilitate interpretation of experimental data and allow for information not readily accessible to experimental methods to be obtained. A large part of the success of empirical force field-based methods is the quality of the force fields combined with the algorithmic advances that allow for more accurate reproduction of experimental observables. Presented is an overview of the issues associated with the development and application of empirical force fields to biomolecular systems. This is followed by a summary of the force fields commonly applied to the different classes of biomolecules; proteins, nucleic acids, lipids, and carbohydrates. In addition, issues associated with computational studies on "heterogeneous" biomolecular systems and the transferability of force fields to a wide range of organic molecules of pharmacological interest are discussed.

DOI10.1002/jcc.20082
Alternate JournalJ Comput Chem
PubMed ID15264253
Grant ListGM51501 / GM / NIGMS NIH HHS / United States