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Results: 1 to 20 of 33

References for PMC Articles for PubMed (Select 21644546)

1.
2.

The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15N chemical shifts.

Spichty M, Taly A, Hagn F, Kessler H, Barluenga S, Winssinger N, Karplus M.

Biophys Chem. 2009 Aug;143(3):111-23. doi: 10.1016/j.bpc.2009.04.003. Epub 2009 Apr 15.

3.

Computational multiscale modeling in protein--ligand docking.

Taufer M, Armen R, Chen J, Teller P, Brooks C.

IEEE Eng Med Biol Mag. 2009 Mar-Apr;28(2):58-69. doi: 10.1109/MEMB.2009.931789. Erratum in: IEEE Eng Med Biol Mag. 2009 May-Jun;28(3):65.

PMID:
19349252
4.

Is quantum mechanics necessary for predicting binding free energy?

Zhou T, Huang D, Caflisch A.

J Med Chem. 2008 Jul 24;51(14):4280-8. doi: 10.1021/jm800242q. Epub 2008 Jun 25.

PMID:
18578469
5.

SFCscore: scoring functions for affinity prediction of protein-ligand complexes.

Sotriffer CA, Sanschagrin P, Matter H, Klebe G.

Proteins. 2008 Nov 1;73(2):395-419. doi: 10.1002/prot.22058.

PMID:
18442132
6.
7.

Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model.

Kolb P, Huang D, Dey F, Caflisch A.

J Med Chem. 2008 Mar 13;51(5):1179-88. doi: 10.1021/jm070654j. Epub 2008 Feb 14.

PMID:
18271520
8.

How to do an evaluation: pitfalls and traps.

Hawkins PC, Warren GL, Skillman AG, Nicholls A.

J Comput Aided Mol Des. 2008 Mar-Apr;22(3-4):179-90. doi: 10.1007/s10822-007-9166-3. Epub 2008 Jan 23. Review. Erratum in: J Comput Aided Mol Des. 2008 Mar-Apr;22(3-4):191-2.

9.

Bias, reporting, and sharing: computational evaluations of docking methods.

Jain AN.

J Comput Aided Mol Des. 2008 Mar-Apr;22(3-4):201-12. Epub 2007 Dec 13.

PMID:
18075713
10.

Benchmarking sets for molecular docking.

Huang N, Shoichet BK, Irwin JJ.

J Med Chem. 2006 Nov 16;49(23):6789-801.

11.

Fragment-based drug design: how big is too big?

Hajduk PJ.

J Med Chem. 2006 Nov 30;49(24):6972-6.

PMID:
17125250
12.

In silico discovery of beta-secretase inhibitors.

Huang D, L├╝thi U, Kolb P, Cecchini M, Barberis A, Caflisch A.

J Am Chem Soc. 2006 Apr 26;128(16):5436-43.

PMID:
16620115
14.

An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes.

Wang R, Lu Y, Fang X, Wang S.

J Chem Inf Comput Sci. 2004 Nov-Dec;44(6):2114-25.

PMID:
15554682
15.

Efficient evaluation of binding free energy using continuum electrostatics solvation.

Huang D, Caflisch A.

J Med Chem. 2004 Nov 4;47(23):5791-7.

PMID:
15509178
16.

Assessing scoring functions for protein-ligand interactions.

Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL 3rd.

J Med Chem. 2004 Jun 3;47(12):3032-47.

PMID:
15163185
17.

Virtual screening using protein-ligand docking: avoiding artificial enrichment.

Verdonk ML, Berdini V, Hartshorn MJ, Mooij WT, Murray CW, Taylor RD, Watson P.

J Chem Inf Comput Sci. 2004 May-Jun;44(3):793-806.

PMID:
15154744
18.

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

Feig M, Karanicolas J, Brooks CL 3rd.

J Mol Graph Model. 2004 May;22(5):377-95.

PMID:
15099834
19.

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.

Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL 3rd.

J Comput Chem. 2004 Jan 30;25(2):265-84.

PMID:
14648625
20.

Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.

Wu G, Robertson DH, Brooks CL 3rd, Vieth M.

J Comput Chem. 2003 Oct;24(13):1549-62.

PMID:
12925999
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