Subject: Scoring-Summary

From: Michele Porro <[email-masked]>
Date: Wed, 05 Mar 2003 15:45:48 +0100

Hello everybody, first of all i would like to thank all of you, who 
answer to my question. I really received a lot of contributions, 
THANKS!!
Best regards
mike

Here a list of the most cited papers on the argument "scoring" :

Böhm, H.-J. (1994). "The development of a simple empirical scoring 
function
to estimate the binding constant for a protein-ligand complex of known
three-dimensional structure." J. Comp. Aid. Mol. Des. 8: 243-256.

Böhm, H.-J. and M. Stahl (1999). "Rapid Empirical Scoring Functions in
Virtual Screening Applications." Med. Chem. Res. 9(7/8): 445-462.

Charifson, P. S., J. J. Corkery, et al. (1999). "Consensus Scoring: A 
Method
for Obtaining Improved Hit Rates from Docking Databases of 
Three-Dimensional
Structures into Proteins." J. Med. Chem. 42: 5100-5109.

Eldridge, M. D., C. W. Murray, et al. (1997). "Empirical scoring 
functions:
I. The development of a fast empirical scoring funciton to estimate the
binding affinity of ligands in receptor complexes." J. Comp. Aid. Mol. 
Des.
11: 425-445.

Gohlke, H., M. Hendlich, et al. (2000). "Knowledge-based Scoring 
Function to
Predict Protein-Ligand Interactions." J. Mol. Biol. 295: 337-356.

Gohlke, H. and G. Klebe (2001). "Statistical potentials and scoring
functions applied to protein-ligand binding." Curr. Opin. Struct. Biol. 
11:
231-235.

Grzybowski, B. A., A. V. Ishchenko, et al. (2002). "From knowledge-based
potentials to combinatorial lead design in silico." Acc Chem Res 35(5):
261-9.

Muegge, I. and Y. C. Martin (1999). "A General and Fast Scoring 
Funciton for
Protein-Lignad Interactions: A Simplified Potential Approach." J. Med. 
Chem.
42: 791-804.

Muegge, I., Y. C. Martin, et al. (1999). "Evaluation of PMF scoring in
docking weak ligands to the FK506 binding protein." J Med Chem 42(14):
2498-503.

Muegge, I. and M. Rarey (2001). Small Molecule Docking and Scoring. 
Reviews
in Computational Chemistry. K. B. Lipkowitz and D. B. Boyd. New York,
Wiley-VCH. 17: 1-60.

Tame, J. R. H. (1999). "Scoring functions: A view from the bench." J. 
Com.
Aid. Mol. Des. 13: 99-108.

Oprea, T. I. and G. R. Marshall (1998). "Receptor-based Prediciton of 
Binding Affinities." Persp. Drug Disc. Des. 9/10/11: 35-61.

Halperin I, Ma B, Wolfson H and Nussinov R. "Principles of Docking: An 
Overview of Search Algorithms and a Guide to Scoring Functions", 
PROTEINS: Structure, Function, and Genetics, 2002; 47:409-443

Stahl, M.; Rarey, M. "Detailed Analysis of Scoring Functions for Virtual
Screening" J. Med. Chem. 44(7) 2001 p1035 - 1042.

Bissantz, C.; Folkers, G.; Rognan, D. "Protein-Based Virtual Screening 
of
Chemical Databases. 1. Evaluation of Different Docking/Scoring
Combinations." J. Med. Chem. 2000, 43, 4759 - 4767.

"The Use of Scoring Functions in Drug Discovery Applications"
Hans-Joachim Bohm and Martin Stahl
Reviews in Computational Chemistry Vol 18, pp 41-87
Eds. Kenny B. Lipkowitz and Donald B. Boyd
Wiley-VCH, 2002

Current Opinion in Structural Biology, Volume 11, Issue2, 1 April 2001, 
pp. 231- 235. G. ... "Statistical potenetials and scoring functions 
applied to protein-ligand binding." H Gohlke, G Klebe.

Current Opinion in Chemical Biology, Volume5, issue4,1 august 2001, p. 
375 - 382. " High-throughput docking for lead generation" R Abagyan, M 
Totrov.

Il Farmaco, vol 57, issue3, March 2002, p. 243 - 251. "Identification 
and mapping of small-molecule binding sites in proteins: computational 
tools for structure-based drug design" C Sotriffer and G Klebe.

H. Goelhke and G. Klebe (2002) Approaches to the description and 
prediction of the binding affinity of small-molecule ligands to 
macromolecular receptors, Angew.Chem.Int.Ed., 41, 2644-2676

Taylor, Jewsbury and Essex (2002) A review of protein-small molecule 
docking methods, Journal of Computer-Aided Molecular Design, 16, 151-166

***************************************
Michele Porro
Institute of Molecular Pharmacy
Pharmacenter
University of Basel
Klingelbergstrasse 50
CH-4056 Basel
Tel:  +41 61 267 15 63
Fax: +41 61 267 15 52
e-mail: [email-masked]
Web : www.pharma.unibas.ch
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