Bibliography¶
- Baber-1992
- Baber, J.C.; Hodgkin, E.E.Automatic Assignment of Chemical Connectivity to Organic Molecules in the Cambridge Structural Database.J. Chem. Inf. Comput. Sci. 1992, 32 (5), 401-406.DOI: 10.1021/ci00009a001
- Balducci-1994
- Balducci, R.; Pearlman, R.S.Efficient Exact Solution of the Ring Perception Problem.J. Chem. Inf. Comput. Sci. 1994, 34 (4), 822-831.DOI: 10.1021/ci00020a016
- Baell-2010
- Baell, J.; Holloway, G.A.New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays.J. Med. Chem. 2010, 53 (7), 2719-2740. DOI: 10.1021/jm901137j
- Baumer-1991
- Baumer, L.; Sala, G.; Sello, G.Ring Perception in Organic Structures: A New Algorithm for Finding SSSR.Comput. Chem. (Oxford, UK) 1991, 15 (4), 293-299.DOI: 10.1016/0097-8485(91)80046-o
- Bemis-1996
- Bemis, G.W.; Murcko, M.A.The Properties of Known Drugs. 1. Molecular Frameworks.J. Med. Chem. 1996, 39 (15), 2887-2893.DOI: 10.1021/jm9602928
- Bertz-1981
- Bertz, S.H.The First General Index of Molecular Complexity.J. Am. Chem. Soc. 1981, 103 (12), 3599-3601.DOI: 10.1021/ja00402a071
- Bissantz-2010
- Bissantz, C.; Kuhn, B.; Stahl, M.A Medicinal Chemist’s Guide to Molecular Interactions.J. Med. Chem. 2010, 53 (14), 5061-5084.DOI: 10.1021/jm100112j
- Blow-2002
- Blow, D.M.Rearrangement of Cruickshank’s Formulae for the Diffraction-Component Precision Index.Acta Crystallogr., Sect. D: Struct. Biol. 2002, 58 (5), 792-797.DOI: 10.1107/s0907444902003931
- Boda-2007
- Boda, K.; Seidel, T.; Gasteiger, J.Structure and Reaction Based Evaluation of Synthetic Accessibility.J. Comput.-Aided Mol. Des. 2007, 21 (6), 311-325.DOI: 10.1007/s10822-006-9099-2
- Bondi-1964
- Bondi, A.van der Waals Volumes and Radii.J. Phys.Chem. 1964, 68 (3), 441-451.DOI: 10.1021/j100785a001
- Brecher-2008
- Brecher, J.Graphical Representation Standards for Chemical Structure Diagrams (IUPAC Recommendations 2008).Pure Appl. Chem. 2008, 80 (2), 277-410.DOI: 10.1351/pac200880020277
- Briem-Lessel-2000
- Briem, H,; Lessel, U.F.In Vitro and in Silico Affinity Fingerprints: Finding Similarities Beyond Structural Classes.Perspect. Drug Discovery Des. 2000, 20 (1), 231–244.DOI: 10.1023/a:1008793325522
- Bunke-2002
- Bunke, H.; Foggia, P.; Guidobaldi, C.; Sansone, C.; Vento, M.A Comparison of Algorithms for Maximum Common Subgraph on Randomly Connected Graphs.Proceedings of the Joint IAPR International Workshop on Structural,Syntactic and Statistical Pattern Recognition.Lecture Notes In Computer Science (LNCS) 2002 2396, 123-132.DOI: 10.1007/3-540-70659-3_12 (OEChem’s MCSS is based upon the ‘’space state search’’ method.)
- Cavallo-2016
- Cavallo, G.; Metrangolo, P.; Milani, R.; Pilati, T.; Priimagi, A.; Resnati, G.; Terraneo, G.The Halogen Bond.Chem.Rev. 2016, 116 (4), 2478-2601.DOI: 10.1021/acs.chemrev.5b00484
- ChEMBL18-2014
- Version ChEMBL_18 from http://www.ebi.ac.uk/chembl (accessed 2014).Primary citation: Gaulton, A.; Bellis, L.J.; Bento, A.P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; et al.ChEMBL: A Large-Scale Bioactivity Database for Drug Discovery.Nucleic Acids Res. 2012, 40 (D1), D1100-D1107.DOI: 10.1093/nar/gkr777 PMID:21948594 (both numbers can be used for structure search within ChEMBL)
- ChEMBL24-2018
- Version ChEMBL_24 from http://www.ebi.ac.uk/chembl (accessed 2018).Primary citation: Gaulton, A.; Hersey, A.; Nowotka, M.; Bento, A.P.; Chambers, J.; Mendez, D.; Mutowo, P.; Atkinson, F.; Bellis, L.J.; Cibrian-Uhalte, E.; et al.The ChEMBL database in 2017.Nucleic Acids Res. 2107, 45 (D1), D945-D954.DOI: 10.1093/nar/gkw1074 PMCID: PMC5210557 (both numbers can be used for structure search within ChEMBL)
- Connolly-1983
- Connolly, M.L.Analytical Molecular Surface Calculation.J. Appl. Crystallogr. 1983, 16 (5), 548-558.DOI: 10.1107/S0021889883010985
- Coutsias-2016
- Coutsias, E.A.; Lexa, K.W.; Wester, M.J.; Pollock, S.N.; Jacobson, M.P.Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics.J. Chem. Theory Comput. 2016, 12 (9), 4674–4687.DOI: 10.1021/acs.jctc.6b00250
- Crippen-1988
- Crippen, G.M.; Havel, T.F.Distance Geometry and Molecular Conformation;Chemometric Series, Vol. 15; Research Studies Press: Taunton, UK, 1988.ISBN: 0471920614, 9780471920618
- Cruickshank-1999
- Cruickshank, D.W.J.Remarks about Protein Structure Precision.Acta Crystallogr., Sect. D: Biol. Crystallogr. 1999, 55 (3), 583-601.DOI: 10.1107/s0907444998012645
- Dayhoff-1978
- Dayhoff, M.O.; Schwartz, R.M.; Orcott, B.C.A Model of Evolutionary Change in Proteins.M.O. Dayhoff(ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington, DC, Vol. 5, pp 345–352, 1978.
- DerevyankoGrudinin-2014
- G. Derevyanko and S. Grudinin,HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions,Acta Crystallographica Section D: Structural Biology, 70 (8), pp.2069-2084, 2014
- Dewar-1985
- M.J.S Dewar, E.G. Zoebisch, E.F. Healy and J.J.P. Stewart,AM1: A New General Purpose Quantum Mechanical Model,Journal of the American Chemical Society, Vol. 107, pp. 3902-3909, 1985.
- Down-1989
- Geoffrey M. Downs, Valerie J. Gillet, John D. Holliday and Michael F. Lynch,Review of Ring Perception Algorithms for Chemical Graphs,Journal of Chemical Information and Computer Science, Vol. 29, pp. 172–187, 1989.
- Dunbrack-1997
- R.L. Dunbrack, Jr., F.E. Cohen,Bayesian statistical analysis of protein side-chain rotamer preferences,Protein Science, Vol. 6 no. 8, pp. 1661–1681, 1997.
- Durant-Leland-2002
- J. L. Durant, B. A. Leland, D. R. Henry and J. G. NourseReoptimization of MDL Keys for Use in Drug Discovery.Journal of Chemical Information and Computer Science, Vol. 42, pp. 1273–1280, 2002,
- 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
- Eldridge-1997
- Matthew D. Eldridge, Christopher W. Murray, Timothy R. Auton, Gaia V.Paolini and Roger P. Mee.,Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes,Journal of Computer-Aided Molecular Design, Vol. 11, pp. 425-445, 1997
- Erickson-2004
- J.A. Erickson, M. Jalaie, D.H. Robertson, R.A. Lewis and M. ViethLessons 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
- 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
- Figueras-1972
- J. Figueras,.Substructure search by set reduction.Journal of Chemical Documentation, Vol. 12 pp. 237–244, 1972.
- Figueras-1996
- John Figueras,Ring Perception Using Breadth-First Search,Journal of Chemical Information and Computer Science, Vol. 36, pp. 986–991, 1996.
- Friedrich-2017
- N. Friedrich, A. Meyder, C. de Bruyn Kops, K. Sommer, F. Flachsenberg, M. Rarey and J. Kirchmair.High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators,|JCIM|, Vol. 57, No. 3, pp. 529-539 2017
- Fujita-1988
- Shinsaku Fujita,A new algorithm for selection of synthetically important rings. The essential set of essential rings for organic structures,Journal of Chemical Information and Computer Science, Vol. 28, pp. 78–82, 1988.
- Gamo-2010
- F. J. Gamo, L. M. Sanz, J. Vidal, C. de Cozar, E. Alvarez, J. L. Lavandera, D. E. Vanderwall,D. V. S. Green, V. Kumar, S. Hasan, J. R. Brown, C. E. Peishoff, L. R. Cardon, J. F. Garcia-Bustos.Thousands of chemical starting points for antimalarial lead identification, Nature, Vol. 465, pp. 305–310, 2010
- Gasteiger-1978
- J. Gasteiger and M. Marsili,A New Model for Calculating Atomic Charges in Molecules,Tetrahedron Letters, pp. 3181-3184, 1978.
- Gasteiger-1979
- Johann Gasteiger and Clemens Jochum,An Algorithm for the Perception of Synthetically Important Rings,Journal of Chemical Information and Computer Science, Vol. 29, pp. 43–48, 1979.
- Gasteiger-1980
- J. Gasteiger and M. Marsili,Iterative Partial Equalization of Orbital Electronegativity - A Rapid Access to Atomic Charges,Tetrahedron, Vol. 36, pp. 3219-3228, 1980.
- Gilson-1988
- M. Gilson, K.A. Sharp, and B. Honig,Calculating the electrostatic potential of molecules in solution: Method and error assessment,Journal of Computational Chemistry, Vol. 9 (4), pp. 327-335, 1988.
- Gonnet-1992
- G.H. Gonnet, M.A. Cohen, and S.A. Benner,Exhaustive matching of the entire protein sequence database,Science, Vol. 256 no. 5062, pp. 1443–1445, 1992.
- Grant-1995
- J.A. Grant and B.T. Pickup,A Gaussian Description of Molecular Shape,Journal of Physical Chemistry, Vol. 99, pp. 3503-3510, 1995.
- Grant-1996
- J.A. Grant, M.A. Gallardo and B.T. Pickup,A fast method of molecular shape comparison. A simple application of a Gaussian description of molecular shape,Journal of Computational Chemistry, Vol. 17, pp. 1653-1666, 1996.
- Grant-1997
- J.A. Grant and B.T. Pickup,Gaussian Shape Methods,Computer Simulation of Biomolecular Systems, Vol 3, 1997.
- Grant-2001
- J.A. Grant, B. Pickup, and A. Nicholls,A smooth permittivity function for Poisson–Boltzmann solvation methods,Journal of Computational Chemistry, Vol. 22 (6), pp. 608-640, 2001.
- Grant-2006
- J. Andrew Grant, James A. Haigh, Barry T. Pickup, Anthony Nicholls and Roger A. Sayle,Lingos, Finite State Machines and Fast Similarity Searching,Journal of Chemical Information and Modeling, Vol. 45, pp. 1912–1918, 2006.
- 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.
- Green-Armytage-2010
- P. Green-Armytage,A Color Alphabet and the Limit of Color Coding,Colors: Design & Creativity., Vol. 6, No. 10, pp. 1–23 2010
- Griffen-2011
- Ed Griffen, Andrew G. Leach, Graeme R. Robb, and Daniel J. Warner,Matched Molecular Pairs as a Medicinal Chemistry Tool,Journal of Medicinal Chemistry, Vol. 54, pp. 7739–7750 2011,
- Grosse-Kunstleve-2002
- R. W. Grosse-Kunstleve, N. K. Sauter, N. W. Moriarty and P. D. Adams,The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework.J. Appl. Cryst., 35, pp. 126-136, 2002.
- 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-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 and 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
- Hamaguchi-2012
- N. Hamaguchi, L. Fusti-Molnar and S. WlodekForce-field and quantum-mechanical binding study of selected SAMPL3 host-guest complexes,Journal of Computer-Aided Molecular Design, Vol. 26, pp. 577-582m 2012
- Hanser-1996
- T. Hanser, P. Jauffret, and G. Kaufmann,A new algorithm for exhaustive ring perception in a molecular graph,Journal of Chemical Information and Computer Science, Vol. 36, pp. 1146–1152, 1996.
- Hare-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
- Hawkins-2007
- Comparison of Shape-Matching and Docking as Virtual Screening ToolsHawkins, P.C.D., Skillman, A.G., Nicholls, A., J.Med. Chem., 2007, 50, 74.
- 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
- Hawkins-2020
- P. C. D. Hawkins, S. J. Wlodek, Decisions With Confidence: Application to the Conformation Sampling of Molecules in the Solid-State,|JCIM|, 2020, submitted
- Henikoff-1992
- S. Henikoff and J.G. Henikoff,Amino acid substitution matrices from protein blocks,Proceedings of the National Academy of Science, USA, Vol. 89 no. 22, pp. 10915–10919, 1992.
- Hert-Willett-2004
- J. Hert, P. Willett and D. J. WiltonComparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures,Journal of Chemical Information and Computer Science, Vol. 44, pp. 1177–1185 2004,
- Hintze-2016
- Bradley J. Hintze, Steven M. Lewis, Jane S. Richardson, David C. Richardson,Molprobity’s ultimate rotamer-library distributions for model validation,Proteins, Vol. 84 pp. 1177–1189, 2016.
- Hussain-2010
- Jameed Hussain and Ceara Rea,Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets,Journal of Chemical Information and Modeling, Vol. 50, pp. 339–348 2010,
- InChI-2013
- (online: http://www.inchi-trust.org/)
- IUPAC-2014
- H.A. Favre, W.H. Powell,Nomenclature of Organic Chemistry - IUPAC Recommendations and Preferred Names 2013,The Royal Society of Chemistry, 2014.
- Jeffrey-1997
- Jeffrey, George A.,An Introduction to Hydrogen Bonding,Oxford University Press,1997
- Kabsch-1983
- W. Kabsch and C. Sander,Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features,Biopolymers, Vol. 22, pp. 2577–2637, 1983.
- Kearsley-1993
- Simon K. Kearsley,A Quick Robust Method for Assigning A Kekulé Structure,Computers in Chemistry, Vol. 17, pp. 1–10, 1993.
- Kelly-1965
- K. Kelly,Twenty-Two Colors of Maximum Contrast,Color Eng., Vol. 3, No. 6, pp. 26–27 1965
- Kramer-2014
- Christian Kramer, Julian, E. Fuchs, Steven Whitebread, Peter Gedeck, and Klaus R. Liedl,Matched Molecular Pair Analysis: Significance and the Impact of Experimental Uncertainty,Journal of Medicinal Chemistry, Vol. 57, pp. 3786–3802 2014,
- Kumar-2002
- S. Kumar and R. Nussinov,Relationship between ion pair geometries and electrostatic strengths in proteins,Biophysical Journal, Vol. 83 no. 3, pp. 1595–1612, 2002.
- Labute-1996-I
- Paul Labute,Automatic Assignment of Bond Order,Journal of the Chemical Computing Group, On-line, May 1996.
- 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
- Lee-Richards-1971
- B. Lee and F. M. RichardsThe interpretation of protein structures: Estimation of static accessibilityJournal of Molecular Biology, Vol. 55, pp. 379–380, 1971
- 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
- Lovell-2000
- Simon C. Lovell, J. Michael Word, Jane S. Richardson, David C. Richardson,The penultimate rotamer library,Proteins, Vol. 40 no. 3, pp. 389–408, 2000.
- Lovell-2003
- Simon C. Lovell, I. W. Davis, W.B. Arendall, P. I. W. De Bakker, J. M. Word, M. G. Prisant, J. S. Richardson, D. C. Richardson,Structure validation by \(C\alpha\) geometry \(\phi\), \(\psi\) and \(C\beta\) deviation.Proteins, Vol. 50 pp. 437–450, 2003.
- 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
- Lloyd-1996
- Douglas Lloyd,What Is Aromaticity?,Journal of Chemical Information and Computer Science, Vol. 36, pp. 442–447, 1996.
- Maier-2015
- J.A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K.E. Hauser and C. Simmerling,** ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB**J. Chem. Theory Comput. 11, pp. 3696-3713, 2015.
- Marcou-2007
- G. Marcou, and D. Rognan,Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction FingerprintsJournal of Chemical Information and Modeling Vol. 47 no. 1, pp. 195–207, 2007
- Markley-1998
- Markley, J.L., Bax, A., Arata, Y., Hilbers, C.W., Kaptein, R., Sykes, B.D., Wright, P.E. and Wüthrich, K.,Recommendations for the presentation of NMR structures of proteins and nucleic acids,Pure and Applied Chemistry, Vol. 70, pp. 117–142, 1998.
- Martin-2005
- Martin, Y.C.,A Bioavailability Score,Journal of Medicinal Chemistry, Vol. 48, pp. 3164-3170, 2005
- Mayne-1998
- L. Mayne, S.W. Englander,R. Qiu, J. Yang, Y. Gong, E.J. Spek and N.R. Kallenbach,Stabilizing Effect of a Multiple Salt Bridge in a Prenucleated Peptide,J. Am. Chem. Soc. Vol. 120, pp. 10643-10645, 1998
- McGann-2003
- Mark McGann, Harold R Almond, Anthony Nicholls, J. Andrew Grant and Frank K. Brown,Gaussian Docking Functions,BioPolymers, Vol. 68, pp. 76-90, 2003
- 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
- McGregor-1982
- James J. McGregor,Backtrack Search Algorithms and the Maximal Common Subgraph Problem,Software – Practice and Experience, Vol. 12, pp. 23–34, 1982.
- McQuarrie-1976
- D.A. McQuarrie,Statistical MechanicsHarper & Row, 1976
- Meng-1991
- Elaine C. Meng and Richard A. Lewis,Determination of Molecular Topology and Atomic Hybridization States from Heavy Atom Coordinates,Journal of Computational Chemistry, Vol. 12, pp. 891–898, 1991.
- 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.
- Mobley-2018
- D.L. Mobley, C.C. Bannan, A. Rizzi, C.I. Bayly, J.D. Chodera, V.T. Lim, N.M. Lim, K.A. Beauchamp, D.R. Slochower, M.R. Shirts, M.K. Gilson, and P.K. Eastman,Escaping Atom Types in Force Fields Using Direct Chemical Perception,J. Chem. Theory Comput., Vol. 14, No. 11, pp. 6076-6092, 2018.
- Muchmore-2008
- Steven W. Muchmore, Derek A. Debe, James T. Metz, Scott P. Brown, Yvonne C. Martin and Philip J. Hajduk,Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping,Journal of Chemical Information and Modeling, Vol. 48, pp. 941–948 2008,
- Mysinger-2012
- Mysinger MM, Carchia M, Irwin JJ, Shoichet BKJ. Med. Chem., 2012, Jul 5.doi 10.1021/jm300687e
- Ndubaku-2009
- C. Ndubaku, E. Varfolomeev, L. Wang, K. Zobel, K. Lau, L. O. Elliot, B. Maurer, A. V. Fedorova, J. N. Dynek,M. Koehler, S. G. Hymowitz, V. Tsui, K. Deshayes, W. J. Fairbrother, J. A. Flygare, D. Vucic.Antagonism of c-IAP and XIAP Proteins Is Required for Efficient Induction of Cell Death by Small-Molecule IAP Antagonists,ACS Chem. Biol., Vol. 4, No. 7, pp. 557–566, 2009
- Nicholls-2008
- Anthony Nicholls, David L. Mobley, J. Peter Guthrie, John D. Chodera, Christopher I. Bayly, Matthew D. Cooper and Vijay S. Pande,Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational ChemistryJournal of Medicinal Chemistry Vol. 51, pp 769-779, 2008.
- Nicholls-2009
- Anthony Nicholls, Stanislaw Wlodek, and J. Andrew GrantThe SAMP1 Solvation Challenge: Further Lessons Regarding the Pitfalls of Parametrization,Journal of Physical Chemistry B, Vol. 113 (14), pp. 4521-4532, 2009.
- Nicholls-2010
- A. Nicholls, S. Wlodek and J.A. Grant,SAMPL2 and continuum modeling,Journal of Computer-Aided Molecular Design, Vol. 24, pp. 293-306, 2010
- Oprea-2000
- Oprea, T.,Property Distribution of Drug-Related Chemical Databases,Journal of Computer-Aided Molecular Design, Vol. 14, pp. 251-264, 2000
- Otter-1989
- A. Otter, P.G. Scott, X.H. Liu and G. Kotovych,A 1H and 13C NMR study on the role of salt-bridges in the formation of a type I beta-turn in N-acetyl-L-Asp-L-Glu-L-Lys-L-Ser-NH2,J. Biomol. Struct. Dyn. Vol. 7, pp. 455-476, 1989
- Papadatos-2010
- George Papadatos, Muhammad Alkarouri, Valerie J. Gillet, Peter Willett,Visakan Kadirkamanathan,Christopher N. Luscombe, Gianpaolo Bravi, Nicola J. Richmond, Stephen D. Pickett,Jameed Hussain, John M. Pritchard, Anthony W.J. Cooper, and Simon J.F. Macdonald,Lead Optimization Using Matched Molecular Pairs: Inclusion of Contextual Information for Enhanced Prediction of hERG Inhibition, Solubility, and Lipophilicity,Journal of Chemical Information and Modeling, Vol. 50, pp. 1872–1886 2010
- Pauling-1960
- Linus Pauling,The Nature of the Chemical Bond and the Structure of Molecules and Crystals; An Introduction to Modern Structural Chemistry,Cornell University Press; 3 edition (1960), ISBN-13: 978-0801403330
- PC-Brown
- Tanimoto combo belief curve, personal communication, Scott Brown, Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, IL.
- PC-Muchmore
- ET combo belief curve, personal communication, Steven W. Muchmore, Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, IL.
- Pierotti-1976
- R.A. Pierotti,A Scaled Particle Theory of Aqueous and Nonaqueous Solutions,Chem. Rev, Vol. 76, pp. 717-726, 1976
- Plotkin-1971
- M. J. Plotkin,Mathematical Basis of Ring-Finding Algorithms in CIDS,Journal of Chemical Documentation, Vol. 11, pp. 60–63, 1971.
- Qian-1990
- C. Qian, W. Fisanick D. E. Hartzler and S. W. Chapman,Enhanced Algorithm for Finding Smallest Set of Smallest Rings,Journal of Chemical Information and Computer Science, Vol. 30, pp. 105–110, 1990.
- Ramachandran-1963
- G.N. Ramachandran, C. Ramakrishnan, V. Sasisekharan,Stereochemistry of polypeptide chain configurations.Journal of Molecular Biology, Vol. 7, pp. 95–99, 1963.
- Rashin-1985
- Alexander A. Rashin, Barry Honig,Reevaluation of the Born model of ion hydration,Journal of Physical Chemistry, Vol. 89, pp. 5588–5593, 1985.
- Raymond-2002
- W. R. Raymond, E.J. Gardiner, and P. Willett,Rascal: Calculation of Graph Similarity Using Maximum Common Edge Subgraphs,The Computer Journal, Vol. 45, pp. 632–644, 2002
- Rippmann-1997
- M. Hendlich, F. Rippmann and G. Barnickel,BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein Databank,Journal of Chemical Information and Computer Science, Vol. 37, pp. 774–778, 1997.
- 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
- Roos-Kozel-1981
- Barbara L. Roos-Kozel and William L. Jorgensen,Computer-Aided Mechanistic Evaluation of Organic Reactions. 2. Perception of Rings, Aromaticity and Tautomers,Journal of Chemical Information and Computer Science, Vol. 21, pp. 101–111, 1981.
- Rossi-2007
- Karen A. Rossi, Carolyn A. Weigelt, Akbar Nayeem and Stanley R. Krystek Jr.,Loopholes and missing links in protein modeling,Protein Science, Vol. 16, pp. 1999–2012, 2007.
- Rush-2005
- A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interactionRush, T.S., Grant, J.A., Mosyak, L., Nicholls, A.,J. Med. Chem., 2005, 48, 1489.
- 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
- Sharp-1990
- K.A. Sharp, and B. Honig,Electrostatic Interactions in Macromolecules: Theory and Applications,Annual Review of Biophysics & Biophysical Chemistry, Vol. 19, pp. 301-332, 1990.
- Sharp-1991
- K.A. Sharp, A. Nicholls, R.F. Fine and B. Honig,Reconciling the Magnitude of the Microscopic and Macroscopic Hydrophobic Effects,Science, Vol. 252 (5002), pp. 106-109, 1991.
- Sheridan-2008
- Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening resultsSheridan, R.P., McGaughey, G.B., Cornell, W.D.,Journal of Computer-Aided Molecular Design, 2008, 22, 257.
- 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
- Sutherland-2007
- Lessons in molecular recognition. 2. Assessing and improving cross-docking accuracySutherland, J.J., Nandigam, R.K., Erickson, J.A., Vieth, M.J. Chem., Inf. Model, 2007, 47, 2293.
- Sutton-1958
- L.E.SuttonTables of Interatomic Distances and Configuration in Molecules and Ions,Chem. Soc., London Special Publication, No.11, 1958
- Takahashi-1994
- Yoshimasa Takahashi,Automatic extraction of ring substructures from a chemical structure,Journal of Chemical Information and Computer Science, 1994, Vol. 34, pp. 167–170, 1994.
- Tuccinardi-2010
- T. Tuccinardi, A. Giordano and A. Martinelli,Protein Kinases: Docking and Homology Modeling ReliabilityJournal of Chemical Information and Modeling, Vol. 50 (8), pp. 1432-1441, 2010
- Ullman-1976
- J.R. Ullman,An Algorithm for Subgraph Isomorphism,Journal of the Association of Computing Machinery (JACM), Vol. 23, pp. 31–42, 1976.
- 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
- Venhorst-2008
- Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction FingerprintsVenhorst, J., Nunez, S., Terpstra, J.W., Kruse, C.G.,J. Med. Chem., 2008, 51, 3222.
- Verkhivker-2000
- Gennady M. Verkhivker, Djamal Bouzida, Daniel K. Gehlhaar, Paul A. Rejto,Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Veda Larson, Brock A. Luty, Tami Marrone and Peter W. Rose,Deciphering common failures in| molecular docking of ligand-protein complexesJournal of Computer-Aided Molecular Design, Vol. 14, pp. 731-751, 2000
- Vidal-2005
- David Vidal, Michael Thormann, and Miquel Pons,LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular SimilaritiesJournal of Chemical Information and Modeling, Vol. 45, pp. 386–393, 2005.
- Vidal-2006
- David Vidal, Michael Thormann, and Miquel Pons,A Novel Search Engine for Virtual Screening of Very Large Databases,Journal of Chemical Information and Modeling, Vol. 46, pp. 836–843, 2006.
- Vincent-2010
- Vincent B. Chen, W. Bryan Arendall III, Jeffrey J. Headd, Daniel A. Keedy, Robert M. Immormino, Gary J. Kapral, Laura W. Murray, Jane S. Richardson, David C. Richardson,MolProbity: all-atom structure validation for macromolecular crystallography.Acta Crystallographica Section D: Structural Biology 66, pp. 12-21, 2010.
- Wang-1997
- T. Wang, and J. Zhou,EMCSS: A New Method for Maximum Common Substructure Search,Journal of Chemical Information and Computer Science, Vol.37 pp. 828–834, 1997.
- 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
- Wang-2000
- J. Wang, P. Cieplak and P.A. Kollman,How well does a Restrained Electrostatic Potential (RESP) model perform in calculating conformational energies of organic and biological molecules?,Journal of Computational Chemistry, Vol. 21, No. 12, pp. 1049-1074, 2000.
- Warner-2010
- Daniel J. Warner, Ed Griffen, and Stephen A. St-Gallay,WizePairZ: A Novel Algorithm to Identify, Encode and Exploit Matched Molecular Pairs with Unspecified Cores in Medicinal Chemistry,Journal of Chemical Information and Modeling, Vol. 50, pp. 1350–1357 2010,
- Warren-2012
- Greg L. Warren, Thanh D. Do, Brian P. Kelley, Anthony Nicholls and Stephen D. Warren,Essential considerations for using protein–ligand structures in drug discovery,Drug Discovery Today, Vol. 17, pp. 1270–1281, 2012.
- 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
- Weininger-1988
- David Weininger,SMILES: A Chemical Language and Information System: 1. Introduction to Methodology and Encoding Rules,Journal of Chemical Information and Computer Science, Vol. 28, pp. 31–36, 1988.
- Weininger-1989
- David Weininger, Arthur Weininger and Joseph L. Weininger,SMILES 2: Algorithm for Generation of Unique SMILES Notation,Journal of Chemical Information and Computer Science, Vol. 29, pp. 97–101, 1989.
- 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: Structural Biology, Vol. 62, pp. 741-749, 2006
- Wiberg-1966
- K.B. Wiberg,Application of the Pople-Santry=Segal CNDO Method to the Cyclopropylcarbinyl and Cyclobutyl Cation and to Bicyclobutane,Tetrahedron, Vol. 24, pp. 1083-1096, 1966.
- Wlodek-2010
- S. Wlodek, A.G. Skillman and A. Nicholls,Ligand entropy in gas-phase, upon solvation and protein complexation. Fast estimation with Quasi-Newton Hessian,J. Chem. Theory Comput., Vol. 6, pp. 2140-2152, 2010
- 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
- Zamora-1979
- Antonio Zamora,An Algorithm for Finding the Smallest Set of Smallest Rings,Journal of Chemical Information and Computer Science, Vol. 16, pp. 40–43, 1976.