• Docs »
  • Bibliography

BibliographyΒΆ

[Bemis-2004]
B.J. Hare, W.P. Walters, P.R. Caron and G.W. Bemis,
CORES: An Automated Method for Generating Three-Dimensional Models of Protein/Ligand Complexes,
Journal of Medicinal Chemistry, Vol. 47 (19), pp. 4731-4740, 2004
[Halgren-I-1996]
T.A. Halgren,
Merck Molecular Force Field: I. Basis, Form, Scope, Parameterization and Performance of MMFF94,
Journal of Computational Chemistry, Vol. 17, No. 5, pp. 490-519, 1996
[Halgren-II-1996]
T.A. Halgren,
Merck Molecular Force Field: II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions,
Journal of Computational Chemistry, Vol. 17, No. 5, pp. 520-552, 1996
[Halgren-III-1996]
T.A. Halgren,
Merck Molecular Force Field: III. Molecular Geometries and Vibrational Frequencies,
Journal of Computational Chemistry, Vol. 17, No. 5, pp. 553-586, 1996
[Halgren-IV-1996]
T.A. Halgren and R.B. Nachbar,
Merck Molecular Force Field: IV. Conformational Energies amd Geometries for MMFF94,
Journal of Computational Chemistry, Vol. 17, No. 5, pp. 687-615, 1996
[Halgren-V-1996]
T.A. Halgren,
Merck Molecular Force Field: V. Extension of MMFF94 using Experimental Data, Additional Computational Data and Empirical Rules,
Journal of Computational Chemistry, Vol. 17, No. 5, pp. 616-641, 1996
[Halgren-VI-1999]
T.A. Halgren,
MMFF VI. MMFF94s Option for Energy Minimization Studies,
Journal of Computational Chemistry, Vol. 20, pp. 720-729, 1999
[Halgren-VII-1999]
T.A. Halgren,
MMFF VII. Characterization of MMFF94, MMFF94s and Other Widely Available Force Fields for Conformational Energies and for Intermolecular Interaction Energies and Geometries,
Journal of Computational Chemistry, Vol. 20, pp. 730-748, 1999
[Hawkins-2010]
P.C.D. Hawkins, A.G. Skillman, G.L. Warren, B.A. Ellingson and M.T. Stahl,
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database,
Journal of Chemical Information and Modeling, Vol. 50 (4), pp. 572-584, 2010
[Martinelli-2010]
T. Tuccinardi, A. Giordano and A. Martinelli,
Protein Kinases: Docking and Homology Modeling Reliability
Journal of Chemical Information and Modeling, Vol. 50 (8), pp. 1432-1441, 2010
[McGann-2003]
McGann, M. R., Almond, H. R., Nicholls, A., Grant, J. A., Brown, F. K.,
Gaussian docking functions,
Biopolymers, Vol. 66, pp 76-90, 2003.
[McGann-2011]
McGann, M. R.,
FRED Pose Prediction and Virtual Screening Accuracy,
Journal of Chemical Information and Modeling, Vol. 51, pp 578-596, 2011.
[McGann-2012]
McGann, M. R.,
FRED and HYBRID docking performance on standardized datasets,
Journal of Computer-Aided Molecular Design, Vol. 26, pp 897-906, 2011.
[MillsDean-1996]
J.E.J. Mills and P.M. Dean,
Three-Dimensional Hydrogen-Bond Geometry and Probability Information from a Crystal Survey,
Journal of Computer-Aided Molecular Design, Vol. 10, pp. 607-622, 1996.
[PDB]
Protein Databank,
[Perola-2004]
E. Perola and P.S. Charifson,
Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding,
J. Med. Chem., Vol. 47, pp. 2499-2510, 2004
[Vieth-2004]
J.A. Erickson, M. Jalaie, D.H. Robertson, R.A. Lewis and M. Vieth
Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy.
Journal of Medicinal Chemistry, Vol. 47 (1), pp. 45-55, 2004
[Warren-2006]
Warren, G. L., Andrews, C. W., Capelli, A.-M. Clarke, B., LaLonde, J., Lambert, M. H., Lindvall, M.,  Nevins, N.,
Semus, S. F., Senger, S., Tedesco, G.,  Wall, I. D.,  Woolven, J. M., Peishoff, C. E.,  and Head,  M. S.,
A Critical Assessment of Docking Programs and Scoring Functions,
Journal of Medicinal Chemistry, Vol. 49, pp 5912-5931, 2006.
[Wlodek-2006]
S. Wlodek, A.G. Skillman and A. Nicholls,
Automated Ligand Placement and Refinement with a Combined Force Field and Shape Potential,
Acta Crystallographica Section D, Vol. 62, pp. 741-749, 2006