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Titolo:
New linear interaction method for binding affinity calculations using a continuum solvent model
Autore:
Zhou, RH; Friesner, RA; Ghosh, A; Rizzo, RC; Jorgensen, WL; Levy, RM;
Indirizzi:
IBM Corp, Thomas J Watson Res Ctr, Yorktown Hts, NY 10598 USA IBM Corp Yorktown Hts NY USA 10598 on Res Ctr, Yorktown Hts, NY 10598 USA Columbia Univ, Dept Chem, New York, NY 10027 USA Columbia Univ New York NY USA 10027 iv, Dept Chem, New York, NY 10027 USA Columbia Univ, Ctr Biomol Simulat, New York, NY 10027 USA Columbia Univ New York NY USA 10027 iomol Simulat, New York, NY 10027 USA Yale Univ, Dept Chem, New Haven, CT 06520 USA Yale Univ New Haven CT USA 06520 Univ, Dept Chem, New Haven, CT 06520 USA Rutgers State Univ, Dept Chem, Piscataway, NJ 08854 USA Rutgers State Univ Piscataway NJ USA 08854 Chem, Piscataway, NJ 08854 USA
Titolo Testata:
JOURNAL OF PHYSICAL CHEMISTRY B
fascicolo: 42, volume: 105, anno: 2001,
pagine: 10388 - 10397
SICI:
1520-6106(20011025)105:42<10388:NLIMFB>2.0.ZU;2-B
Fonte:
ISI
Lingua:
ENG
Soggetto:
MOLECULAR-DYNAMICS SIMULATIONS; SELECTIVE ANTI-HIV-1 AGENTS; INTERACTION ENERGY METHOD; MONTE-CARLO SIMULATIONS; FAST MULTIPOLE METHOD; AIDED DRUG DESIGN; RESPONSE METHOD; 1-<(2-HYDROXYETHOXY)METHYL>-6-(PHENYLTHIO)THYMINE HEPT; ANTIVIRAL ACTIVITY; INHIBITOR BINDING;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
47
Recensione:
Indirizzi per estratti:
Indirizzo: Zhou, RH IBM Corp, Thomas J Watson Res Ctr, Route 134 & POB 218, Yorktown Hts, NY 10598 USA IBM Corp Route 134 & POB 218 Yorktown Hts NY USA 10598 10598 USA
Citazione:
R.H. Zhou et al., "New linear interaction method for binding affinity calculations using a continuum solvent model", J PHYS CH B, 105(42), 2001, pp. 10388-10397

Abstract

A new linear interaction energy (LIE) method based on a continuum solvent surface generalized Born (SGB) model is proposed for protein-ligand bindingaffinity calculations. The new method SGB-LIE is about 1 order of magnitude faster than previously published LIE methods based on explicit solvents. It has been applied to several binding sets: HEPT analogues binding to HIV-1 reverse transcriptase (20 ligands), sulfonamide inhibitors binding to human thrombin (seven ligands), and various ligands binding to coagulation factor Xa (eight ligands). The SGB-LIE predictions and cross-validation results show that about 1.0 kcal/mol accuracy is achievable for binding sets withas many as 20 ligands, e.g., for the HIV-1 RT binding set, RMS errors of 1.07 and 1.20 kcal/mol are achieved for LIE fitting and leave-one-out cross validation, respectively, with correlation coefficients r(2) equal to 0.774and 0.717. We have also explored various techniques for the LIE underlyingconformation space sampling, including molecular dynamics and hybrid MonteCarlo methods, and the final results show that comparable binding energiescan be obtained no matter which sampling technique is used.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 03/04/20 alle ore 19:55:19