Customized versus universal scoring functions: Application to class I MHC-peptide binding free energy predictions

被引：38

作者：

Logean, A

Sette, A

Rognan, D ^{[1
]}

机构：

[1] UMR 7081, Lab Pharmacochim Commun Cellulaire, F-67401 Illkirch Graffenstaden, France

[2] Epimmune Inc, San Diego, CA 92121 USA

来源：

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS | 2001年 / 11卷 / 05期

关键词：

D O I：

10.1016/S0960-894X(01)00021-X

中图分类号：

R914 [药物化学];

学科分类号：

100701 ;

摘要：

A tailor-made free energy scoring method (Fresno) has been compared to six universal scoring functions (Chemscore, Dock, FlexX, Gold, Pmf, Score) for predicting the binding affinity of 26 peptides to the class I human major histocompatibility protein HLA-B*2705. Fresno clearly outperforms all six universal scoring functions. (C) 2001 Elsevier Science Ltd. All rights reserved.

引用

收藏

页码：675 / 679

页数：5

相关论文

共 26 条

[1] A structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets [J].

Altuvia, Y ;

Sette, A ;

Sidney, J ;

Southwood, S ;

Margalit, H .

HUMAN IMMUNOLOGY, 1997, 58 (01) :1-11

[2] 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

[3] IMPORTANCE OF PEPTIDE AMINO AND CARBOXYL TERMINI TO THE STABILITY OF MHC CLASS-I MOLECULES [J].

BOUVIER, M ;

WILEY, DC .

SCIENCE, 1994, 265 (5170) :398-402

[4] Description and prediction of peptide-MHC binding: the 'human MHC project' [J].

Buus, S .

CURRENT OPINION IN IMMUNOLOGY, 1999, 11 (02) :209-213

[5] A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES [J].

CORNELL, WD ;

CIEPLAK, P ;

BAYLY, CI ;

GOULD, IR ;

MERZ, KM ;

FERGUSON, DM ;

SPELLMEYER, DC ;

FOX, T ;

CALDWELL, JW ;

KOLLMAN, PA .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) :5179-5197

[6] Empirical scoring functions .1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes [J].

Eldridge, MD ;

Murray, CW ;

Auton, TR ;

Paolini, GV ;

Mee, RP .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1997, 11 (05) :425-445

[7]

Ewing TJA, 1997, J COMPUT CHEM, V18, P1175, DOI 10.1002/(SICI)1096-987X(19970715)18:9<1175::AID-JCC6>3.0.CO

[8]

2-O

[9] CRYSTAL-STRUCTURE OF AN H-2K(B)-OVALBUMIN PEPTIDE COMPLEX REVEALS THE INTERPLAY OF PRIMARY AND SECONDARY ANCHOR POSITIONS IN THE MAJOR HISTOCOMPATIBILITY COMPLEX BINDING GROOVE [J].

FREMONT, DH ;

STURA, EA ;

MATSUMURA, M ;

PETERSON, PA ;

WILSON, IA .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1995, 92 (07) :2479-2483

[10] On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions [J].

Froloff, N ;

Windemuth, A ;

Honig, B .

PROTEIN SCIENCE, 1997, 6 (06) :1293-1301