From chemistry-request@server.ccl.net Mon Mar 3 15:12:23 2003 Received: from mxout4.cac.washington.edu ([140.142.33.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h23KCNQ12787 for ; Mon, 3 Mar 2003 15:12:23 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout4.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.12) with ESMTP id h23KCFHV023445 for ; Mon, 3 Mar 2003 12:12:15 -0800 Received: from DGVR6B21 ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with SMTP id h23KCFwZ015788 for ; Mon, 3 Mar 2003 12:12:15 -0800 Message-ID: <00bb01c2e1c1$317fc4f0$74805f80@DGVR6B21> From: "Carsten Detering" To: Subject: CCL:Scoring Date: Mon, 3 Mar 2003 21:12:19 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00B8_01C2E1C9.9331B660" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_00B8_01C2E1C9.9331B660 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Michele, try these: B=F6hm, 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. B=F6hm, 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" To: "CCL" 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 > Pharmacenter > University of Basel > Klingelbergstrasse 50 > CH-4056 Basel > Tel: +41 61 267 15 63 > Fax: +41 61 267 15 52 > e-mail: michele.porro@unibas.ch > Web : www.pharma.unibas.ch > **************************************** > > > > -=3D This is automatically added to each message by mailing script = =3D- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > ------=_NextPart_000_00B8_01C2E1C9.9331B660 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi=20 Michele,



try these:

B=F6hm, H.-J. (1994). "The = development=20 of a simple empirical scoring function
to estimate the binding = constant for a=20 protein-ligand complex of known
three-dimensional structure." J. = Comp. Aid.=20 Mol. Des. 8: 243-256.

B=F6hm, H.-J. and M. Stahl (1999). "Rapid = Empirical=20 Scoring Functions in
Virtual Screening Applications." Med. Chem. Res. = 9(7/8):=20 445-462.

Charifson, P. S., J. J. Corkery, et al. (1999). = "Consensus=20 Scoring: A Method
for Obtaining Improved Hit Rates from Docking = Databases of=20 Three-Dimensional
Structures into Proteins." J. Med. Chem. 42:=20 5100-5109.

Eldridge, M. D., C. W. Murray, et al. (1997). = "Empirical=20 scoring functions:
I. The development of a fast empirical scoring = funciton to=20 estimate the
binding affinity of ligands in receptor complexes." J. = Comp.=20 Aid. Mol. Des.
11: 425-445.

Gohlke, H., M. Hendlich, et al. = (2000).=20 "Knowledge-based Scoring Function to
Predict Protein-Ligand = Interactions." J.=20 Mol. Biol. 295: 337-356.

Gohlke, H. and G. Klebe (2001). = "Statistical=20 potentials and scoring
functions applied to protein-ligand binding." = Curr.=20 Opin. Struct. Biol. 11:
231-235.

Grzybowski, B. A., A. V. = Ishchenko,=20 et al. (2002). "From knowledge-based
potentials to combinatorial lead = design=20 in silico." Acc Chem Res 35(5):
261-9.

Muegge, I. and Y. C. = Martin=20 (1999). "A General and Fast Scoring Funciton for
Protein-Lignad = Interactions:=20 A Simplified Potential Approach." J. Med. Chem.
42: = 791-804.

Muegge,=20 I., Y. C. Martin, et al. (1999). "Evaluation of PMF scoring = in
docking weak=20 ligands to the FK506 binding protein." J Med Chem=20 42(14):
2498-503.

Muegge, I. and M. Rarey (2001). Small = Molecule=20 Docking and Scoring. Reviews
in Computational Chemistry. K. B. = Lipkowitz and=20 D. B. Boyd. New York,
Wiley-VCH. 17: 1-60.

Tame, J. R. H. = (1999).=20 "Scoring functions: A view from the bench." J. Com.
Aid. Mol. Des. = 13:=20 99-108.

Oprea, T. I. and G. R. Marshall (1998). "Receptor-based Prediciton of = Binding=20 Affinities." Persp. Drug Disc. Des. 9/10/11: 35-61.



Hope this helps.
Carsten


----- = Original=20 Message -----
From: "Michele Porro" <
michele.porro@unibas.ch>
To: "CCL" <
chemistry@ccl.net
>
Sent: Monday, March 03, 2003 = 11:19=20 AM
Subject: CCL:Scoring


> Hallo = everybody,
>  =20 could somebody of you suggest me good review-papers on scoring = and
>=20 scoring functions? I would like to find out which are the most = used
>=20 procedures to score docking results.
> Thank you in advace
> = Best=20 regards
> mike
>
>=20 ***************************************
> Michele Porro
> = Institute=20 of Molecular Pharmacy
> Pharmacenter
> University of = Basel
>=20 Klingelbergstrasse 50
> CH-4056 Basel
> Tel:  +41 61 = 267 15=20 63
> Fax: +41 61 267 15 52
> e-mail: michele.porro@unibas.ch
> Web : www.pharma.unibas.ch
>=20 ****************************************
>
>
>
> = -=3D This=20 is automatically added to each message by mailing script =3D-
> = CHEMISTRY@ccl.net -- To=20 Everybody  | CHEMISTRY-REQUEST@ccl.net -- To
Admins
> Ftp: = ftp.ccl.net  | =20 WWW: http://www.ccl.net/chemistry/   | Jan:
jkl@ccl.net
>
>
>
>
>
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