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Items: 1 to 20 of 27

1.

DARS (Decoys As the Reference State) potentials for protein-protein docking.

Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S.

Biophys J. 2008 Nov 1;95(9):4217-27. doi: 10.1529/biophysj.108.135814. Epub 2008 Aug 1.

2.

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding.

Young T, Abel R, Kim B, Berne BJ, Friesner RA.

Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):808-13. Epub 2007 Jan 4.

3.

PIPER: an FFT-based protein docking program with pairwise potentials.

Kozakov D, Brenke R, Comeau SR, Vajda S.

Proteins. 2006 Nov 1;65(2):392-406.

PMID:
16933295
4.

Characterization of protein-ligand interaction sites using experimental and computational methods.

Vajda S, Guarnieri F.

Curr Opin Drug Discov Devel. 2006 May;9(3):354-62. Review.

PMID:
16729732
5.

Multiple solvent crystal structures: probing binding sites, plasticity and hydration.

Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D.

J Mol Biol. 2006 Apr 14;357(5):1471-82. Epub 2006 Jan 30.

PMID:
16488429
6.

A method for localizing ligand binding pockets in protein structures.

Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM.

Proteins. 2006 Feb 1;62(2):479-88.

PMID:
16304646
7.
8.

Druggability indices for protein targets derived from NMR-based screening data.

Hajduk PJ, Huth JR, Fesik SW.

J Med Chem. 2005 Apr 7;48(7):2518-25.

PMID:
15801841
9.

Pocketome via comprehensive identification and classification of ligand binding envelopes.

An J, Totrov M, Abagyan R.

Mol Cell Proteomics. 2005 Jun;4(6):752-61. Epub 2005 Mar 9.

10.

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

Laurie AT, Jackson RM.

Bioinformatics. 2005 May 1;21(9):1908-16. Epub 2005 Feb 8.

PMID:
15701681
11.

Identification of substrate binding sites in enzymes by computational solvent mapping.

Silberstein M, Dennis S, Brown L, Kortvelyesi T, Clodfelter K, Vajda S.

J Mol Biol. 2003 Oct 3;332(5):1095-113.

PMID:
14499612
12.

Structure-based design of aliskiren, a novel orally effective renin inhibitor.

Wood JM, Maibaum J, Rahuel J, Grütter MG, Cohen NC, Rasetti V, Rüger H, Göschke R, Stutz S, Fuhrer W, Schilling W, Rigollier P, Yamaguchi Y, Cumin F, Baum HP, Schnell CR, Herold P, Mah R, Jensen C, O'Brien E, Stanton A, Bedigian MP.

Biochem Biophys Res Commun. 2003 Sep 5;308(4):698-705.

PMID:
12927775
13.

Computational mapping identifies the binding sites of organic solvents on proteins.

Dennis S, Kortvelyesi T, Vajda S.

Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4290-5. Epub 2002 Mar 19.

14.

Unraveling hot spots in binding interfaces: progress and challenges.

DeLano WL.

Curr Opin Struct Biol. 2002 Feb;12(1):14-20. Review.

PMID:
11839484
15.

Experimental and computational mapping of the binding surface of a crystalline protein.

English AC, Groom CR, Hubbard RE.

Protein Eng. 2001 Jan;14(1):47-59.

PMID:
11287678
16.

Is there a future for renin inhibitors?

Fisher ND, Hollenberg NK.

Expert Opin Investig Drugs. 2001 Mar;10(3):417-26. Review.

PMID:
11227042
17.

Structure-based drug design: the discovery of novel nonpeptide orally active inhibitors of human renin.

Rahuel J, Rasetti V, Maibaum J, Rüeger H, Göschke R, Cohen NC, Stutz S, Cumin F, Fuhrer W, Wood JM, Grütter MG.

Chem Biol. 2000 Jul;7(7):493-504.

18.

Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol.

English AC, Done SH, Caves LS, Groom CR, Hubbard RE.

Proteins. 1999 Dec 1;37(4):628-40.

PMID:
10651278
19.

The Protein Data Bank.

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE.

Nucleic Acids Res. 2000 Jan 1;28(1):235-42.

20.

Locating and characterizing binding sites on proteins.

Mattos C, Ringe D.

Nat Biotechnol. 1996 May;14(5):595-9. Review.

PMID:
9630949

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