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Items: 1 to 20 of 106

2.

SHEF: a vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces.

Cai W, Xu J, Shao X, Leroux V, Beautrait A, Maigret B.

J Mol Model. 2008 May;14(5):393-401. doi: 10.1007/s00894-008-0286-z.

PMID:
18330602
3.

Protein flexibility in ligand docking and virtual screening to protein kinases.

Cavasotto CN, Abagyan RA.

J Mol Biol. 2004 Mar 12;337(1):209-25.

PMID:
15001363
4.
5.

A fast surface-matching procedure for protein-ligand docking.

Yamagishi ME, Martins NF, Neshich G, Cai W, Shao X, Beautrait A, Maigret B.

J Mol Model. 2006 Sep;12(6):965-72.

PMID:
16673083
6.

Examination of shape complementarity in docking of unbound proteins.

Norel R, Petrey D, Wolfson HJ, Nussinov R.

Proteins. 1999 Aug 15;36(3):307-17.

PMID:
10409824
7.

Optimization of high throughput virtual screening by combining shape-matching and docking methods.

Lee HS, Choi J, Kufareva I, Abagyan R, Filikov A, Yang Y, Yoon S.

J Chem Inf Model. 2008 Mar;48(3):489-97. doi: 10.1021/ci700376c.

PMID:
18302357
8.

Small molecule recognition: solid angles surface representation and molecular shape complementarity.

Norel R, Wolfson HJ, Nussinov R.

Comb Chem High Throughput Screen. 1999 Aug;2(4):223-37.

PMID:
10469882
9.

HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.

Floriano WB, Vaidehi N, Zamanakos G, Goddard WA 3rd.

J Med Chem. 2004 Jan 1;47(1):56-71.

PMID:
14695820
10.

Molecular docking using surface complementarity.

Sobolev V, Wade RC, Vriend G, Edelman M.

Proteins. 1996 May;25(1):120-9.

PMID:
8727324
11.

A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): theory and application.

Baroni M, Cruciani G, Sciabola S, Perruccio F, Mason JS.

J Chem Inf Model. 2007 Mar-Apr;47(2):279-94.

PMID:
17381166
12.

Fully automated molecular mechanics based induced fit protein-ligand docking method.

Koska J, Spassov VZ, Maynard AJ, Yan L, Austin N, Flook PK, Venkatachalam CM.

J Chem Inf Model. 2008 Oct;48(10):1965-73. doi: 10.1021/ci800081s.

PMID:
18816046
13.
15.

SDOCKER: a method utilizing existing X-ray structures to improve docking accuracy.

Wu G, Vieth M.

J Med Chem. 2004 Jun 3;47(12):3142-8.

PMID:
15163194
16.

Docking by least-squares fitting of molecular surface patterns.

Bacon DJ, Moult J.

J Mol Biol. 1992 Jun 5;225(3):849-58.

PMID:
1602486
17.

Fragment-Based flexible ligand docking by evolutionary optimization.

Budin N, Majeux N, Caflisch A.

Biol Chem. 2001 Sep;382(9):1365-72.

PMID:
11688719
18.

Effect of crystal freezing and small-molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 A resolution.

Skrzypczak-Jankun E, Borbulevych OY, Zavodszky MI, Baranski MR, Padmanabhan K, Petricek V, Jankun J.

Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):766-75.

PMID:
16790932
19.

An evaluation of spherical designs for molecular-like surfaces.

Morris RJ.

J Mol Graph Model. 2006 Mar;24(5):356-61.

PMID:
16275031
20.

LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites.

Venkatachalam CM, Jiang X, Oldfield T, Waldman M.

J Mol Graph Model. 2003 Jan;21(4):289-307.

PMID:
12479928

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