Empirical force fields for biological macromolecules: overview and issues.
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.
Mackerell
Alexander D
AD
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA. alex@outerbanks.umaryland.edu
D000465:Algorithms; D002241:Carbohydrates / Q000737:chemistry*; D003198:Computer Simulation; D008055:Lipids / Q000737:chemistry*; D046911:Macromolecular Substances; D008958:Models, Molecular; D009696:Nucleic Acids / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D002241:Carbohydrates; D008055:Lipids; D046911:Macromolecular Substances; D009696:Nucleic Acids; D011506:Proteins