Subject: CCL:Scoring

From: "Carsten Detering" <[email-masked]>
Date: Mon, 3 Mar 2003 21:12:19 +0100

Hi Michele,

try these:

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.

Hope this helps.
Carsten

----- Original Message -----
From: "Michele Porro" <[email-masked]>
To: "CCL" <[email-masked]>
Sent: Monday, March 03, 2003 11:19 AM
Subject: CCL:Scoring

> Hallo everybody,
>   could somebody of you suggest me good review-papers on scoring and
> scoring functions? I would like to find out which are the most used
> procedures to score docking results.
> Thank you in advace
> Best regards
> mike
>
> ***************************************
> Michele Porro
> Institute of Molecular Pharmacy
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> University of Basel
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> Fax: +41 61 267 15 52
> e-mail: [email-masked]
> Web : www.pharma.unibas.ch
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>
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