A new method for predicting binding affinity in computer-aided drug design

A new semi–empirical method for calculating free energies of binding from molecular dynamics (MD) simulations is presented. It is based on standard thermodynamic cycles and on a linear approximation of polar and non–polar free energy contributions from the corresponding MD averages. The method is te...

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Veröffentlicht in:	Protein engineering 1994-03, Vol.7 (3), p.385-391
Hauptverfasser:	Åqvist, Johan, Medina, Carmen, Samuelsson, Jan-Erik
Format:	Artikel
Sprache:	eng
Schlagworte:	Aspartic Acid Endopeptidases - antagonists & inhibitors binding free energies Binding Sites Biological and medical sciences Biotechnology Computer Simulation Drug Design Electrochemistry endothiapepsin Fundamental and applied biological sciences. Psychology General pharmacology inhibitor binding Medical sciences molecular dynamics simulation Molecular Structure Pharmaceutical technology. Pharmaceutical industry Pharmacology. Drug treatments Protein Binding Thermodynamics
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Beschreibung
Zusammenfassung:	A new semi–empirical method for calculating free energies of binding from molecular dynamics (MD) simulations is presented. It is based on standard thermodynamic cycles and on a linear approximation of polar and non–polar free energy contributions from the corresponding MD averages. The method is tested on a set of endothiapepsin inhibitors and found to give accurate results both for absolute as well as relative free energies.
ISSN:	1741-0126 0269-2139 1741-0134 1460-213X
DOI:	10.1093/protein/7.3.385