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Titolo:
A NEW METHOD FOR PREDICTING BINDING FREE-ENERGY BETWEEN RECEPTOR AND LIGAND
Autore:
TAKAMATSU Y; ITAI A;
Indirizzi:
INST MED MOL DESIGN,BUNKYO KU,5-24-5 HONGO TOKYO 113 JAPAN UNIV TOKYO,FAC PHARMACEUT SCI TOKYO 113 JAPAN
Titolo Testata:
Proteins
fascicolo: 1, volume: 33, anno: 1998,
pagine: 62 - 73
SICI:
0887-3585(1998)33:1<62:ANMFPB>2.0.ZU;2-U
Fonte:
ISI
Lingua:
ENG
Soggetto:
ESCHERICHIA-COLI; DIHYDROFOLATE-REDUCTASE; L-ARABINOSE; 3-DIMENSIONAL STRUCTURE; COMPUTATIONAL METHOD; MOLECULAR MECHANICS; AQUEOUS-SOLUTION; NUCLEIC-ACIDS; SUGAR-BINDING; FORCE-FIELD;
Keywords:
DRUG DESIGN; RECEPTOR-LIGAND INTERACTION; COMPUTER SIMULATION; SOLVATION ENERGY; DESOLVATION ENERGY;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Science Citation Index Expanded
Science Citation Index Expanded
Citazioni:
47
Recensione:
Indirizzi per estratti:
Citazione:
Y. Takamatsu e A. Itai, "A NEW METHOD FOR PREDICTING BINDING FREE-ENERGY BETWEEN RECEPTOR AND LIGAND", Proteins, 33(1), 1998, pp. 62-73

Abstract

A practical method to estimate binding free energy, Delta G(bind), Ofa given ligand structure to the target receptor has been developed. The method assumes that Delta G(bind) is given by the summation of intermolecular interaction energy, Delta G(inter) and partial desolvation energy, Delta G(desolv). Delta G(desolv) is calculated from the buriedsurface area in the complex between the ligand and receptor, based onsolvation energy, Delta G(solv), formulated by an equation which can be calibrated with observed values. Then, the method was applied to arabinose-binding protein (ABP) and dihydrofolate reductase (DHFR), after recalibrating the weights for dG(inter) and each term of Delta G(desolv) using observed Delta G(bind) data for 29 known ligands to avidin (AV). The usefulness of our method was confirmed by the fact that correlation coefficients between the calculated and observed Delta G(bind')S in AV, ABP and DHFR were 0.92, 0.77, and 0.88, whereas the corresponding values obtained by simple force field calculation were 0.79, 0.30, and 0.79, respectively. Further investigations to improve the method and validate the parameters are in progress. (C) 1998 Wiley-Liss, Inc.

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Documento generato il 02/04/20 alle ore 00:11:56