Bibliography¶
- Coutsias-2016
- E. A. Coutsias, K. W. Lexa, M. J. Wester, S. N. Pollock, M. P. Jacobson,Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics,J. Chem. Theory Comput., Vol. 12, pp. 4674–4687, 2016
- Crippen-1988
- G. M. Crippen, T. F. Havel,Distance Geometry and Molecular Conformation,Chemometric Series, Vol. 15, Research Studies Press: Taunton, UK, 1988
- 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
- Guba-2016
- W. Guba, A. Meyder, M. Rarey and J. Hert,Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules,Journal of Chemical Information and Modeling, Vol. 56, pp. 1-5, 2016
- 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 and 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
- 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, No. 4, pp 572-584, 2010
- Labute-2010
- P. Labute,LowModeMD - Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops,Journal of Chemical Information and Modeling, Vol. 50, pp 792–800, 2010
- 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-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
- Watts-2014
- K.S. Watts, P. Dalal, A.J. Tebben, D.L. Cheney, and J.C. Shelley,Macrocycle Conformational Sampling with MacroModel,Journal of Chemical Information and Modeling, Vol. 54, pp 2680–2696, 2014
- Baell-2010
- Baell, J. and Holloway, G.A.,New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays,Journal of Medicinal Chemistry, Vol 53, pp. 2719-2740, 2010
- 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
- Jeffrey, George A.,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
- Lovering, F., Bikker, J. and Humblet, C.,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
- Ritchie-2009
- Ritchie, Timothy J. and Macdonald, Simon J.F.,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-1997-2
- 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
- Yalkowsky-1980
- Yalkowsky, S.H. and Valvani, S.C.,Solubility and Partitioning 1: Solubility of Nonelectrolytes in Water,Journal of Pharmaceutical Sciences, Vol. 69, pp. 912-922, 1980