BibliographyΒΆ

[Bostrom-2001]Jonas Bostrom, Reproducing the Conformations of Protein-Bound Ligands: A Critical Evaluation of Several Popular Conformational Searching Tools, Journal of Computer-Aided Molecular Design (JCAMD), Vol. 15, pp. 1137, 2001
[Bostrom-2003]J. Bostrom, J.R. Greenwood, and J. Gottfries, Assessing the Performance of OMEGA with Respect to Retrieving Bioactive Conformations, Journal of Molecular Graphics and Modeling, Vol. 21, pp. 449–462, 2003
[Gasteiger-1990]J. Gasteiger, C. Rudolph and J. Sadowski, Automatic Generation of 3D Atomic Coordinates for Organic Molecules, Tetrahedron Comp. Method, Vol 3., pp. 537-547, 1990
[Gasteiger-1993]J. Sadowski and J. Gasteiger, From Atoms and Bonds to Three-dimensional Atomic Coordinates: Automatic Model Builders, Chemical Reviews, Vol. 93, pp. 2567-2581, 1993
[Grant-2001]J. Andrew Grant, Anthony Nicholls, A. Geoffrey Skillman, and Matthew T. Stahl, Dude, where are my conformers?, 222nd National ACS Meeting, 2001
[Grant-2007]J.A. Grant, B.T. Pickup, M.J. Sykes, C.A. Kitchen and A. Nicholls, A Simple Formula for Dielectric Polarization Energies: The Sheffield Solvation Model, Chem. Phys. Letters, Vol. 441, pp. 163-166, 2007
[Halgren-1996-1]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-1996-2]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-1996-3]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-1996-4]T.A. Halgren, Merck Molecular Force Field: IV. Conformational Energies amd Geometries for MMFF94, Journal of Computational Chemistry, Vol. 17, No. 5, pp. 587-615, 1996
[Halgren-1996-5]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-1999-1]T.A. Halgren, MMFF VI. MMFF94s Option for Energy Minimization Studies, Journal of Computational Chemistry, Vol. 20, No. 5, pp. 720-729, 1999
[Halgren-1999-2]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, No. 5, 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, J. Chem. Inf. Model., Vol. 50, No. 4, pp 572-584, 2010
[Sadowski-1994]J. Sadowski, J. Gasteiger and G. Klebe, Comparison of Automatic Three-dimensional Model Builders using 639 X-Ray Structures, Journal of Chemical Information and Computer Science (JCICS), Vol. 34, pp. 1000-1008, 1994
[Spellmeyer-1997]David C. Spellmeyer, A.K. Wong, M.J. Bower and J.M. Blaney, Conformational Analysis using Distance Geometry Methods, Journal of Molecular Graphics and Modeling, Vol. 15, No. 1, pp. 18-36 1997
[Stahl-2000]Matthew T. Stahl, Rapid 3D Database Searching, IIR: Computational Drug Design, 2000
[Stahl-2001]Matthew T. Stahl, You want conformers? I’ll give you conformers!, 2nd Annual OpenEye Customers, Users, and Programmers Meeting, 2001
[Stahl-2002]Matthew T. Stahl, Omega, AESOP, and other cautionary tales of naming programs., 3rd Annual OpenEye Customers, Users, and Programmers Meeting, 2002
[Clark-1999]Clark, D.E., Rapid Calculation of Polar Molecular Surface Area and its Application to the Prediction of Transport Phenomena. 1. Prediction of Intestinal Absorption, Journal of Pharmaceutical Sciences, Vol. 88, pp. 807-814, 1999
[Egan-2000]Egan, W.J., Merz, K.M. and Baldwin, J.J., Prediction of Drug Absorption Using Multivariate Statistics, Journal of Medicinal Chemistry, Vol. 43, pp. 3867-3877, 2000
[Ertl-2000]Ertl, P., Rohde, B., and Selzer, P., Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and its Application to the Prediction of Drug Transport Properties, Journal of Medicinal Chemistry, Vol. 43, pp. 3714-3717, 2000
[Jeffrey-1997]George A. Jeffrey, An Introduction to Hydrogen Bonding, Oxford University Press, 1997
[Lipinski-1997]Lipinski, C.A., Lombardo, F., Dominy, B.W. and Feeney, P.J., Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings, Advanced Drug Delivery Reviews, Vol. 23, pp. 3-25, 1997
[Lovering-2009]Frank Lovering, Jack Bikker, and Christine Humblet, Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success, Journal of Medicinal Chemistry, 52 (21):6752-6756
[Martin-2005]Martin, Y.C., A Bioavailability Score, Journal of Medicinal Chemistry, Vol. 48, pp. 3164-3170, 2005
[McGovern-2003]McGovern S.L., Helfand, B.T., Feng, B. and Shoichet, B.K., A Specific Mechanism of Nonspecific Inhibition, Journal of Medicinal Chemistry, Vol. 46, pp. 4265-4272, 2003
[MillsDean-1996]Mills, J.E.J and Dean, P.M., Three-Dimensional Hydrogen-Bond Geometry and Probability Information from a Crystal Survey, Journal of Computer-Aided Molecular Design, Vol. 10, pp. 607-622, 1996
[Oprea-2000]Oprea, T., Property Distribution of Drug-Related Chemical Databases, Journal of Computer-Aided Molecular Design, Vol. 14, pp. 251-264, 2000
[Rishton-2003]Rishton, G.M., Nonleadlikeness and Leadlikeness in Biochemical Screening, Drug Discovery Today, Vol. 8, pp. 86-96, 2003
[Ritchie-2009]Timothy J. Ritchie and Simon J.F. Macdonald, The impact of aromatic ring count on compound developability - are too many aromatic rings a liability in drug design?, Drug Discovery Today, 14(21):1011
[Seidler-2003]Seidler J., McGovern, S.L., Doman, T.N. and Shoichet, B.K., Identification and Prediction of Promiscuous Aggregating Inhibitors Among Known Drugs, Journal of Medicinal Chemistry, Vol. 46, pp. 4477-4486, 2003
[Veber-2002]Veber, D.F., Johnson, S.R., Cheng, H.Y., Smith, B.R., Ward, K.W. and Kopple, K.D., Molecular Properties that Influence the Oral Bioavailability of Drug Candidates, Journal of Medicinal Chemistry, Vol. 45, pp. 2615-2623, 2002
[Wang-1997]Wang, R., Ying, F., and Lai, L., A New Atom-Additive Method for Calculating Partition Coefficients, Journal of Chemical Information and Computer Science, Vol. 37, pp. 615-621, 1997
[Wishart-2006]Wishart, D.S., DrugBank: A Comprehensive Resource For In Silico Drug Discovery and Exploration, Nucleic Acids Research, Vol. 34, pp. D668-672, 2006
[Yalkowsky-1980]Yalkowsky, S.H. and Valvani, S.C., Solubility and Partitioning 1: Solubility of Nonelectorlytes in Water, Journal of Pharmaceutical Sciences, Vol. 69, pp. 912-922, 1980

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