Warning: The NCBI web site requires JavaScript to function. more...
Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock.
Bikadi Z, Hazai E.
J Cheminform. 2009 Sep 11;1:15.
Related citations
Using AutoDock for ligand-receptor docking.
Morris GM, Huey R, Olson AJ.
Curr Protoc Bioinformatics. 2008 Dec;Chapter 8:Unit 8.14.
Estimates of ligand-binding affinities supported by quantum mechanical methods.
Söderhjelm P, Kongsted J, Genheden S, Ryde U.
Interdiscip Sci. 2010 Mar;2(1):21-37. Epub 2010 Jan 28.
A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets.
Mukherjee G, Patra N, Barua P, Jayaram B.
J Comput Chem. 2011 Apr 15;32(5):893-907. doi: 10.1002/jcc.21671. Epub 2010 Oct 22.
Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach.
Cho AE, Guallar V, Berne BJ, Friesner R.
J Comput Chem. 2005 Jul 15;26(9):915-31.
Assessing the role of polarization in docking.
Illingworth CJ, Morris GM, Parkes KE, Snell CR, Reynolds CA.
J Phys Chem A. 2008 Nov 27;112(47):12157-63.
A model binding site for testing scoring functions in molecular docking.
Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK.
J Mol Biol. 2002 Sep 13;322(2):339-55.
Partial charge calculation method affects CoMFA QSAR prediction accuracy.
Mittal RR, Harris L, McKinnon RA, Sorich MJ.
J Chem Inf Model. 2009 Mar;49(3):704-9.
pso@autodock: a fast flexible molecular docking program based on Swarm intelligence.
Namasivayam V, Günther R.
Chem Biol Drug Des. 2007 Dec;70(6):475-84. Epub 2007 Nov 6.
The effect of different electrostatic potentials on docking accuracy: a case study using DOCK5.4.
Tsai KC, Wang SH, Hsiao NW, Li M, Wang B.
Bioorg Med Chem Lett. 2008 Jun 15;18(12):3509-12. Epub 2008 May 10.
A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands.
Fanfrlík J, Bronowska AK, Rezác J, Prenosil O, Konvalinka J, Hobza P.
J Phys Chem B. 2010 Oct 7;114(39):12666-78.
Extension of QM/MM docking and its applications to metalloproteins.
Cho AE, Rinaldo D.
J Comput Chem. 2009 Dec;30(16):2609-16.
J Comput Chem. 2010 Oct 22. [Epub ahead of print]
ProPose: a docking engine based on a fully configurable protein-ligand interaction model.
Seifert MH, Schmitt F, Herz T, Kramer B.
J Mol Model. 2004 Dec;10(5-6):342-57. Epub 2004 Oct 8.
PSI-DOCK: towards highly efficient and accurate flexible ligand docking.
Pei J, Wang Q, Liu Z, Li Q, Yang K, Lai L.
Proteins. 2006 Mar 1;62(4):934-46.
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database.
Plewczynski D, Łaźniewski M, Augustyniak R, Ginalski K.
J Comput Chem. 2011 Mar;32(4):742-55. doi: 10.1002/jcc.21643. Epub 2010 Sep 1.
Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.
Zoete V, Grosdidier A, Cuendet M, Michielin O.
J Mol Recognit. 2010 Sep-Oct;23(5):457-61.
In silico mutagenesis and docking studies of Pseudomonas aeruginosa PA-IIL lectin predicting binding modes and energies.
Adam J, Kríz Z, Prokop MP, Wimmerová M, Koca J.
J Chem Inf Model. 2008 Nov;48(11):2234-42.
Efficient docking of peptides to proteins without prior knowledge of the binding site.
Hetényi C, van der Spoel D.
Protein Sci. 2002 Jul;11(7):1729-37.
Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.
Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C.
J Chem Inf Model. 2009 Jun;49(6):1455-74.
Filter your results:
Your browsing activity is empty.
Activity recording is turned off.
Turn recording back on