Fast and accurate predictions of relative binding energies

被引：9

作者：

Alex, A

Finn, P

机构：

[1] Pfizer Central Research, Ramsgate Road, Sandwich

来源：

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM | 1997年 / 398卷

关键词：

binding energy; scoring functions; prediction;

D O I：

10.1016/S0166-1280(97)00031-6

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

We report on the development of a fast, empirical method for estimating the binding affinity of protein-ligand complexes. The method is of comparable accuracy to existing empirical methods, but uses fewer parameters. We also report on experiments, using a combined quantum mechanical/molecular mechanical (QM/MM) approach, applied to a dataset of thermolysin inhibitors, with improved performance. (C) 1997 Elsevier Science B.V.

引用

收藏

页码：551 / 554

页数：4

相关论文

共 25 条

[1]

ALEX A, UNPUB

[2] NEW METHOD FOR PREDICTING BINDING-AFFINITY IN COMPUTER-AIDED DRUG DESIGN [J].

AQVIST, J ;

MEDINA, C ;

SAMUELSSON, JE .

PROTEIN ENGINEERING, 1994, 7 (03) :385-391

[3] POSSIBLE ROLE FOR WATER DISSOCIATION IN THE SLOW BINDING OF PHOSPHORUS-CONTAINING TRANSITION-STATE-ANALOGUE INHIBITORS OF THERMOLYSIN [J].

BARTLETT, PA ;

MARLOWE, CK .

BIOCHEMISTRY, 1987, 26 (26) :8553-8561

[4] DEFINITION AND DISPLAY OF STERIC, HYDROPHOBIC, AND HYDROGEN-BONDING PROPERTIES OF LIGAND-BINDING SITES IN PROTEINS USING LEE AND RICHARDS ACCESSIBLE SURFACE - VALIDATION OF A HIGH-RESOLUTION GRAPHICAL TOOL FOR DRUG DESIGN [J].

BOHACEK, RS ;

MCMARTIN, C .

JOURNAL OF MEDICINAL CHEMISTRY, 1992, 35 (10) :1671-1684

[5]

Bohm H J, 1993, J Mol Recognit, V6, P131, DOI 10.1002/jmr.300060305

[6] ON THE USE OF LUDI TO SEARCH THE FINE CHEMICALS DIRECTORY FOR LIGANDS OF PROTEINS OF KNOWN 3-DIMENSIONAL STRUCTURE [J].

BOHM, HJ .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1994, 8 (05) :623-632

[7] THE DEVELOPMENT OF A SIMPLE EMPIRICAL SCORING FUNCTION TO ESTIMATE THE BINDING CONSTANT FOR A PROTEIN LIGAND COMPLEX OF KNOWN 3-DIMENSIONAL STRUCTURE [J].

BOHM, HJ .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1994, 8 (03) :243-256

[8] PEPTIDE MIMETICS AS ENZYME-INHIBITORS - USE OF FREE-ENERGY PERTURBATION CALCULATIONS TO EVALUATE ISOSTERIC REPLACEMENT FOR AMIDE BONDS IN A POTENT HIV PROTEASE INHIBITOR [J].

CIEPLAK, P ;

KOLLMAN, PA .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1993, 7 (03) :291-304

[9] DETERMINATION OF THE RELATIVE BINDING FREE-ENERGIES OF PEPTIDE INHIBITORS TO THE HIV-1 PROTEASE [J].

FERGUSON, DM ;

RADMER, RJ ;

KOLLMAN, PA .

JOURNAL OF MEDICINAL CHEMISTRY, 1991, 34 (08) :2654-2659

[10] MOLECULAR-DYNAMICS SIMULATION WITH A CONTINUUM ELECTROSTATIC MODEL OF THE SOLVENT [J].

GILSON, MK .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1995, 16 (09) :1081-1095