Bibliography

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
Bento-2014
Bento, A.P.; Gaulton, A.; Hersey, A.; Bellis, L.J.; Chambers, J.; Davies, M.; Krüger, F.A.; Light, Y.; Mak, L.; McGlinchey, S.; et al.
The ChEMBL Bioactivity Database: an Update.
Nucleic Acids Res. 2014, 42 (D1), D1083–D1090.
DOI: 10.1093/nar/gkt1031
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
Bertz-1982
Bertz, S.H.
Convergence, Molecular Complexity, and Synthetic Analysis.
J. Am. Chem. Soc. 1982, 104 (21), 5801–5803.
DOI: 10.1021/ja00385a049
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
Boström-2001
Boström, J.
Reproducing the Conformations of Protein-Bound Ligands: A Critical Evaluation of Several Popular Conformational Searching Tools.
J. Comput.-Aided Mol. Des. 2001, 15 (12), 1137–1152.
DOI: 10.1023/a:1015930826903
Boström-2003
Boström, J.; Greenwood, J.R.; Gottfries, J.
Assessing the Performance of OMEGA with Respect to Retrieving Bioactive Conformations.
J. Mol. Graphics Modell. 2003, 21 (5), 449–462.
DOI: 10.1016/s1093-3263(02)00204-8
Brown-Muchmore-2008
Brown, S.; Muchmore, S.W., Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, IL.
Belief Curves for Tanimoto Combo and Electrostatic Tanimoto Combo.
Personal Communication, 2008.
Cascarano-1991
Cascarano, G.; Giacovazzo, C.; Camalli, M.; Spagna, R; Watkin, D.
Automatic Solution and Refinement of Crystal Structures by Means of the Package UNIQUE.
Acta Crystallogr., Sect. A: Found. Crystallogr. 1991, A47 (4), 373–381.
DOI: 10.1107/s010876739100096x
Chen-2003
Chen, X.; Wang, W.
The Use of Bioisosteric Groups in Lead Optimization.
In Annu. Rep. Med. Chem., Vol. 38; Elsevier, Inc., 2003; pp. 333–346.
DOI: 10.1016/S0065-7743(03)38033-9
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.
J. Pharm. Sci. 1999, 88 (8), 807–814.
DOI: 10.1021/js9804011
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; Research Studies Press, 1988.
Dallal-2001
Dallal, G.E.
The Little Handbook of Statistical Practice; Kindle, 2012.
Amazon ID (ASIN): B00847SM6A.
(Originally cited as http://www.StatisticalPractice.com, accessed May 2011.)
Diller-1999
Diller, D.J.; Verlinde, C.L.M.J.
A Critical Evaluation of Several Global Optimization Algorithms for the Purpose of Molecular Docking.
J. Comput. Chem. 1999, 20 (16), 1740–1751.
DOI: 10.1002/(sici)1096-987x(199912)20:16<1740::aid-jcc6>3.0.co;2-a
DOCK
The Official UCSF DOCK Website. http://dock.compbio.ucsf.edu/
Durant-2002
Durant, J.L.; Leland, B.A.; Henry, D.R.; Nourse, J.G.
Reoptimization of MDL Keys for Use in Drug Discovery.
J. Chem. Inf. Comput. Sci. 2002, 42 (6), 1273–1280.
DOI: 10.1021/ci010132r
Egan-2000
Egan, W.J.; Merz, K.M.; Baldwin, J.J.
Prediction of Drug Absorption Using Multivariate Statistics.
J. Med. Chem. 2000, 43 (21), 3867–3877.
DOI: 10.1021/jm000292e
Eisenberg-1986
Eisenberg, D.; McLachlan, A.D.
Solvation Energy in Protein Folding and Binding.
Nature 1986, 319 (6050), 199–203.
DOI: 10.1038/319199a0
Eldridge-1997
Eldridge, M.D.; Murray, C.W.; Auton, T.R.; Paolini, G.V.; Mee, R.P.
Empirical Scoring Functions: I. The Development of a Fast Empirical Scoring Function to Estimate the Binding Affinity of Ligands in Receptor Complexes.
J. Comput.-Aided Mol. Des. 1997, 11 (5), 425–445.
DOI: 10.1023/a:1007996124545
Erickson-2004
Erickson, J.A.; Jalaie, M.; Robertson, D.H.; Lewis, R.A.; Vieth, M.
Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy.
J. Med. Chem. 2004, 47 (1), 45–55.
DOI: 10.1021/jm030209y
Ertl-2000
Ertl, P.; Rohde, B.; 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.
J. Med Chem. 2000, 43 (20), 3714–3717.
DOI: 10.1021/jm000942e
Fletterick-1982
Fletterick, R.J.; Matela, R.
Color-Coded ⍺-Carbon Models of Proteins.
Biopolymers 1982, 21 (5), 999–1003.
DOI: https://doi.org/10.1002/bip.360210512
Friedrich-2017
Friedrich, N.-O.; Meyder, A.; de Bruyn Kops, C.; Sommer, K.; Flachsenberg, F.; Rarey, M.; Kirchmair, J.
High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators.
J. Chem. Inf. Model. 2017 57, (3), 529–539.
DOI: 10.1021/acs.jcim.6b00613
Gamo-2010
Gamo, F.-J.; Sanz, L.M.; Vidal, J.; de Cozar, C.; Alvarez, E.; Lavandera, J.-L.; Vanderwall, D.E.;
Green, D.V.S.; Kumar, V.; Hasan, S.; et al.
Thousands of Chemical Starting Points for Antimalarial Lead Identification.
Nature 2010, 465 (7296), 305–310.
DOI: 10.1038/nature09107
Grant-1995
Grant, J.A.; Pickup,B.T.
A Gaussian Description of Molecular Shape.
J. Phys.Chem. 1995, 99 (11), 3503–3510.
DOI: 10.1021/j100011a016
Grant-1996
Grant, J.A.; Gallardo, M.A.; Pickup, B.T.
A Fast Method of Molecular Shape Comparison. A Simple Application of a Gaussian Description of Molecular Shape.
J. Comput. Chem. 1996, 17 (14), 1653–1666.
DOI: 10.1002/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K
Grant-1997
Grant, J.A.; Pickup, B.T.
Gaussian Shape Methods. In: Computer Simulations of Biomolecular Systems, Vol 3;
van Gunsteren, W.F., Weiner, P.K., Wilkinson, A.J., Eds.; Springer, 1997; pp. 150–176.
DOI: 10.1007/978-94-017-1120-3_5
Grant-2001
Grant, J.A.; Pickup, B.T.; Nicholls, A.
A Smooth Permittivity Function for Poisson–Boltzmann Solvation Methods.
J. Comput. Chem. 2001, 22 (6), 608–640.
DOI: 10.1002/jcc.1032
Grant-2007
Grant, J.A.; Pickup, B.T.; Sykes, M.J.; Kitchen, C.A.; Nicholls, A.
A Simple Formula for Dielectric Polarization Energies: The Sheffield Solvation Model.
Chem. Phys. Lett. 2007, 441 (1–3), 163–166.
DOI: 10.1016/j.cplett.2007.05.008
GraphSim
GraphSim TK OpenEye, Cadence Molecular Sciences
GRID
Molecular Discovery. http://www.moldiscovery.com/soft_grid.php
Guba-2016
Guba, W.; Meyder, A.; Rarey, M.; Hert, J.
Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules.
J. Chem. Inf. Model. 2016, 56 (1), 1–5.
DOI: 10.1021/acs.jcim.5b00522
Guillot-2002
Guillot, B.
A Reappraisal of What We Have Learnt During Three Decades of Computer Simulations on Water.
J. Mol. Liq. 2002, 101 (1–3), 219–260.
DOI: 10.1016/s0167-7322(02)00094-6
Hajduk-2007
Hajduk, P.J.; Greer, J.
A Decade of Fragment-Based Drug Design: Strategic Advances and Lessons Learned.
Nat. Rev. Drug Discovery 2007, 6 (3), 211–219.
DOI: 10.1038/nrd2220
Halgren-I-1996
Halgren, T.A.
Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94.
J. Comput. Chem. 1996, 17 (5–6), 490–519.
DOI: 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P
Halgren-II-1996
Halgren, T.A.
Merck Molecular Force Field. II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions.
J. Comput. Chem. 1996, 17 (5–6), 520–552.
DOI: 10.1002/(SICI)1096-987X(199604)17:5/6<520::AID-JCC2>3.0.CO;2-W
Halgren-III-1996
Halgren, T.A.
Merck Molecular Force Field: III. Molecular Geometries and Vibrational Frequencies for MMFF94.
J. Comput. Chem. 1996, 17 (5–6), 553–586.
DOI: 10.1002/(SICI)1096-987X(199604)17:5/6<553::AID-JCC3>3.0.CO;2-T
Halgren-IV-1996
Halgren, T.A.; Nachbar, R.B.
Merck Molecular Force Field. IV. Conformational Energies and Geometries for MMFF94.
J. Comput. Chem. 1996, 17 (5–6), 587–615.
DOI: 10.1002/(SICI)1096-987X(199604)17:5/6<587::AID-JCC4>3.0.CO;2-Q
Halgren-V-1996
Halgren, T.A.
Merck Molecular Force Field. V. Extension of MMFF94 using Experimental Data, Additional Computational Data, and Empirical Rules.
J. Comput. Chem. 1996, 17 (5–6), 616–641.
DOI: 10.1002/(SICI)1096-987X(199604)17:5/6<616::AID-JCC5>3.0.CO;2-X
Halgren-VI-1999
Halgren, T.A.
MMFF VI. MMFF94s Option for Energy Minimization Studies.
J. Comput. Chem. 1999, 20 (7), 720–729.
DOI: 10.1002/(SICI)1096-987X(199905)20:7<720::AID-JCC7>3.0.CO;2-X
Halgren-VII-1999
Halgren, T.A.
MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Available Force Fields for Conformational Energies and for Intermolecular-Interaction Energies and Geometries.
J. Comput. Chem. 1999, 20 (7), 730–748.
DOI: 10.1002/(SICI)1096-987X(199905)20:7<730::AID-JCC8>3.0.CO;2-T
Hanley-1982
Hanley, J.A.; McNeil, B.J.
The Meaning and Use of the Area Under a Receiver Operating Characteristic (ROC) Curve.
Radiology 1982, 143 (1), 29–36.
DOI: 10.1148/radiology.143.1.7063747
Hare-2004
Hare, B.J.; Walters, W.P.; Caron, P.R.; Bemis, G.W.
CORES: An Automated Method for Generating Three-Dimensional Models of Protein/Ligand Complexes.
J. Med. Chem. 2004, 47 (19), 4731–4740.
DOI: 10.1021/jm0499054
Hawkins-2010
Hawkins, P.C.D.; Skillman, A.G.; Warren, G.L.; Ellingson, B.A.; Stahl, M.T.
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database.
J. Chem. Inf. Model. 2010, 50 (4), 572–584.
DOI: 10.1021/ci100031x
Hawkins-2020
Hawkins, P.C.D.; Wlodek, S.J.
Decisions With Confidence: Application to the Conformation Sampling of Molecules in the Solid State.
J. Chem. Inf. Model. 2020, 60 (7), 3518–3533.
DOI: 10.1021/acs.jcim.0c00358
Hermann-1972
Hermann, R.B.
Theory of Hydrophobic Bonding. II. Correlation of Hydrocarbon Solubility in Water With Solvent Cavity Surface Area.
J. Phys. Chem. 1972, 76 (19), 2754–2759.
DOI: 10.1021/j100663a023
Huang-2003
Huang, X.; Margulis, C.J.; Berne, B.J.
Dewetting-Induced Collapse of Hydrophobic Particles.
Proc. Natl. Acad. Sci. U. S. A. 2003, 100 (21), 11953–11958.
DOI: 10.1073/pnas.1934837100
Huang-2006
Huang, N.; Shoichet, B.K.; Irwin, J.J.
Benchmarking Sets for Molecular Docking.
J. Med. Chem. 2006, 49 (23), 6789–6801.
DOI: 10.1021/jm0608356
Jain-2008
Jain, A.N.; Nicholls, A.
Recommendations for Evaluation of Computational Methods.
J. Comput-Aided Mol. Des. 2008, 22 (3–4), 133–139.
DOI: 10.1007/s10822-008-9196-5
Jakalian-2000
Jakalian, A.; Bush, B.L.; Jack, D.B.; Bayly, C.I.
Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: I: Method.
J. Comput. Chem. 2000, 21 (2), 132–146.
DOI: 10.1002/(sici)1096-987x(20000130)21:2%3C132::aid-jcc5%3E3.0.co;2-p
Jakalian-2002
Jakalian, A.; Jack, D.B.; Bayly, C.I.
Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: II. Parameterization and Validation.
J. Comput. Chem. 2002, 23 (16), 1623–1641.
DOI: 10.1002/jcc.10128
Jeffrey-1997
Jeffrey, G.A.
An Introduction to Hydrogen Bonding;
Oxford University Press, 1997.
ISBN: 0195095499, 9780195095494
Jones-1991
Jones, T.A.; Zou, J.-Y.; Cowan, S.W.; Kjeldgaard, M.
Improved Methods for Building Protein Models in Electron Density Maps and the Location of Errors in these Models.
Acta Crystallogr., Sect. A: Found. Crystallogr. 1991, A47 (2), 110–119.
DOI: 10.1107/s0108767390010224
Kleywegt-2004
Kleywegt, G.J.; Harris, M.R.; Zou, J.-Y.; Taylor, T.C.; Wählby, A.; Jones, T.A.
The Uppsala Electron-Density Server.
Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, D60 (12), 2240–2249.
DOI: 10.1107/s0907444904013253
Koch-1974
Koch, M.H.
On the Application of Phase Relationships to Complex Structures. VI. Automatic Interpretation of Electron-Density Maps for Organic Structures.
Acta Crystallogr., Sect. A: Cryst. Phys., Diffr., Theor. Gen. Crystallogr. 1974, A30 (1), 67–70.
DOI: 10.1107/s0567739474000118
Labute-2010
Labute, P.
LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops.
J. Chem. Inf. Model. 2010, 50 (5), 792–800.
DOI: 10.1021/ci900508k
Lauri-1994
Lauri, G.; Bartlett, P.A.
CAVEAT: A Program to Facilitate the Design of Organic Molecules.
J. Comput.-Aided Mol. Des. 1994 8 (1), 51–66.
DOI: 10.1007/bf00124349
Lewell-1998
Lewell, X.Q.; Judd, D.B.; Watson, S,P; Hann, M.M.
RECAP—Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments With Useful Applications in Combinatorial Chemistry.
J. Chem. Inf. Comput. Sci. 1998, 38 (3), 511–522.
DOI: 10.1021/ci970429i
Lipinski-1997
Lipinski, C.A.; Lombardo, F.; Dominy, B.W; Feeney, P.J.
Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings.
Adv. Drug Delivery Rev. 1997, 23 (1–3), 3–25.
DOI: 10.1016/s0169-409x(96)00423-1
Lovering-2009
Lovering, F.; Bikker, J.; Humblet, C.
Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success.
J. Med. Chem. 2009, 52 (21), 6752–6756.
DOI: 10.1021/jm901241e
Martin-2005
Martin, Y.C.
A Bioavailability Score.
J. Med. Chem. 2005, 48 (9), 3164–3170.
DOI: 10.1021/jm0492002
…. [Masek-1993]
Masek, B.B.; Merchant, A.; Matthew, J.B.
Molecular Shape Comparison of Angiotensin II Receptor Antagonists.
J. Med. Chem. 1993, 36 (9), 1230–1238.
DOI: 10.1021/jm00061a014
Mayne-1998
Mayne, L.; Englander, S.W.; Qiu, R.; Yang, J.; Gong, Y.; Spek, E.J.; Kallenbach, N.R.
Stabilizing Effect of a Multiple Salt Bridge in a Prenucleated Peptide.
J. Am. Chem. Soc. 1998, 120 (41), 10643–10645.
DOI: 10.1021/ja981592c
McGann-2003
McGann, M.; Almond, H.R.; Nicholls, A.; Grant, J.A.; Brown, F.K.
Gaussian Docking Functions.
Biopolymers 2003, 68 (1), 76–90.
DOI: 10.1002/bip.10207
McGovern-2003
McGovern, S.L.; Helfand, B.T.; Feng, B.; Shoichet, B.K.
A Specific Mechanism of Nonspecific Inhibition.
J. Med. Chem. 2003, 46 (20), 4265–4272.
DOI: 10.1021/jm030266r
McQuarrie-1976
McQuarrie, D.A.
Statistical Mechanics;
Harper & Row, 1976.
Menéndez-Velázquez-2003
Menéndez-Velázquez, A.; García-Granda, S.
A Procedure Towards the Automatic Solution of Crystal Structures by Means of Topological Analysis of Fourier Maps.
J. Appl. Crystallogr. 2003, 36 (2), 193–205.
DOI: 10.1107/s0021889802022100
Mills-Dean-1996
Mills, J.E.J.; Dean, P.M.
Three-Dimensional Hydrogen-Bond Geometry and Probability Information from a Crystal Survey.
J. Comput.-Aided Mol. Des. 1996, 10 (6), 607–622.
DOI: 10.1007/bf00134183
Mobley-2018
Mobley, D.L.; Bannan, C.C.; Rizzi, A.; Bayly, C.I.; Chodera, J.D.; Lim, V.T.; Lim, N.M.; Beauchamp, K.A.; Slochower, D.R.; Shirts, M.R.; et al.
Escaping Atom Types in Force Fields Using Direct Chemical Perception.
J. Chem. Theory Comput. 2018, 14 (11), 6076–6092.
DOI: 10.1021/acs.jctc.8b00640
Muchmore-2008
Muchmore, S.W.; Debe, D.A.; Metz, J.T.; Brown, S.P.; Martin, Y.C.; Hajduk, P.J.
Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping.
J. Chem.Inf. Model. 2008, 48 (5), 941–948.
DOI: 10.1021/ci7004498
Nicholls-1991
Nicholls, A.; Sharp, K.A.; Honig, B.
Protein Folding and Association: Insights from the Interfacial and Thermodynamic Properties of Hydrocarbons.
Proteins: Struct., Funct., Bioinf. 1991, 11, (4), 281–96.
DOI: 10.1002/prot.340110407
Nicholls-2008
Nicholls,A.; Mobley, D.L.; Guthrie, J.P.; Chodera, J.D.; Bayly, C.I.; Cooper, M.D.; Pande, V.S.
Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry.
J. Med. Chem. 2008, 51 (4), 769–779.
DOI: 10.1021/jm070549+
Nicholls-2009
Nicholls, A.; Wlodek, S.; Grant, J.A.
The SAMP1 Solvation Challenge: Further Lessons Regarding the Pitfalls of Parametrization.
J. Phys. Chem. B 2009, 113 (14), 4521–4532.
DOI: 10.1021/jp806855q
Nicholls-2010
Nicholls, A.; Wlodek S.; Grant, J.A.
SAMPL2 and Continuum Modeling.
J. Comput.-Aided Mol. Des. 2010, 24 (4), 293–306.
DOI: 10.1007/s10822-010-9334-8
Oldfield-2001
Oldfield, T.J.
Creating Structure Features by Data Mining the PDB to Use as Molecular-Replacement Models.
Acta Crystallogr., Sect. D: Biol. Crystallogr. 2001, D57 (10), 1421–1427.
DOI: 10.1107/s0907444901012483
Oprea-2000
Oprea, T.
Property Distribution of Drug-Related Chemical Databases.
J. Comput.-Aided Mol. Des. 2000, 14 (3), 251–264.
DOI: 10.1023/a:1008130001697
Otter-1989
Otter, A.; Scott, P.G.; Liu, X.H.; Kotovych, G.
A 1H and 13C NMR Study on the Role of Salt-Bridges in the Formation of a Type I ß-Turn in N-Acetyl-L-Asp-L-Glu-L-Lys-L-Ser-NH2.
J. Biomol. Struct. Dyn. 1989, 7 (3), 455–476.
DOI: 10.1080/07391102.1989.10508504
Perola-2004
Perola, E.; Charifson, P.S.
Conformational Analysis of Drug-Like Molecules Bound to Proteins: an Extensive Study of Ligand Reorganization upon Binding.
J. Med. Chem. 2004, 47 (10), 2499–2510.
DOI: 10.1021/jm030563w
PDB-IDs
RCSB Protein Databank. https://www.rcsb.org/ (accessed May 2011)
Trypsin inhibitors:
PDB ID: 1C2D Citation: Katz, B.A., Luong, C. Recruiting Zinc to Mediate Potent, Specific Inhibition of Serine Proteases (1999) doi 10.2210/pdb1C2D/pdb
PDB ID: 1C5T Citation: Katz, B.A., Mackman, R., Luong, C., Radika, K., Martelli, A., Sprengeler, P.A., Wang, J., Chan, H., Wong, L. Structural Basis for Selectivity of a Small Molecule, S1-Binding, Sub-Micromolar Inhibitor of Urokinase Type Plasminogen Activator (1999) doi 10.2210/pdb1C5T/pdb
PDB ID: 1F0T Citation: Maignan, S., Guilloteau, J.P., Pouzieux, S., Choi-Sledeski, Y.M., Becker, M.R., Klein, S.I., Ewing, W.R., Pauls, H.W., Spada, A.P., Mikol, V. Bovine Trypsin Complexed with RPR131247 (2000) doi 10.2210/pdb1F0T/pdb
PDB ID: 1G3D Citation: Toyota, E., Ng, K.K.S., Sekizaki, H., Itoh, K., Tanizawa, K., James, M.N.G. Bovine Beta-Trypsin Bound to Meta-Amidino Schiff Base Copper (II) Chelate (2000) doi 10.2210/pdb1G3D/pdb
PDB ID: 1G3E Citation: Toyota, E., Ng, K.K.S., Sekizaki, H., Itoh, K., Tanizawa, K., James, M.N.G. Bovine Beta-Trypsin Bound to Para-Amidino Schiff Base Copper (II) Chelate (2000) doi 10.2210/pdb1G3E/pdb
PDB ID: 1GHZ Citation: Katz, B.A., Elrod, K., Luong, C., Rice, M., Mackman, R.L., Sprengeler, P.A., Spencer, J., Hatayte, J., Janc, J., Link, J., Litvak, J., Rai, R., Rice, K., Sideris, S., Verner, E., Young, W. A Novel Serine Protease Inhibition Motif Involving a Multi-Centered Short Hydrogen Bonding Network at the Active Site (2001) doi 10.2210/pdb1GHZ/pdb
PDB ID: 1GJ6 Citation: Katz, B.A., Sprengeler, P.A., Luong, C., Verner, E., Spencer, J.R., Breitenbucher, J.G., Hui, H., McGee, D., Allen, D., Martelli, A., Mackman, R.L. Engineering Inhibitors Highly Selective for the S1 Sites of SER190 Trypsin-Like Serine Protease Drug Targets (2001) doi 10.2210/pdb1GJ6/pdb
PDB ID: 1H4W Citation: Katona, G., Berglund, G.I., Hajdu, J., Graf, L., Szilagyi, L. Structure of human trypsin IV (brain trypsin) (2001) doi 10.2210/pdb1H4W/pdb
PDB ID: 1J17 Citation: Stubbs, M.T. Factor XA Specific Inhibitor in Complex with Rat Trypsin Mutant X99/175/190RT (2002) doi 10.2210/pdb1J17/pdb
PDB ID: 1K1I Citation: Stubbs, M.T. Bovine Trypsin-Inhibitor Complex (2001) doi 10.2210/pdb1K1I/pdb
PDB ID: 1K1L Citation: Stubbs, M.T. Bovine Trypsin-Inhibitor Complex (2001) doi 10.2210/pdb1K1L/pdb
PDB ID: 1K1N Citation: Stubbs, M.T. Bovine Trypsin-Inhibitor Complex (2001) doi 10.2210/pdb1K1N/pdb
PDB ID: 1PPC Citation: Bode, W., Turk, D. Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-alpha-(2-naphthyl-sulphonyl-glycyl)-DL-P-amidinophenylalanyl-oiperidine (NAPAP) and (2R,4R)-4-methy-1-[N-alpha-(3-methyl-1,2,3,4-tetrahydro-8-quinolinesulphonyl)-L-arginyl]-2-piperidine Carboxylic Acid (MQPA) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the NAPAP-Trypsin Complex and Modeling of NAPAP-Thrombin AND MQPA-Thrombin (1991) doi 10.2210/pdb1PPC/pdb
PDB ID: 1QB1 Citation: Whitlow, M. Bovine Trypsin with 1-[2-[5-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5-dihydro-1-methyl-1H-imidazol-2-yl)phenoxy]pyridin-4-yl]piperidine-3-carboxylic Acid (ZK-806974) (1999) doi 10.2210/pdb1QB1/pdb
PDB ID: 1QB6 Citation: Whitlow, M. Bovine Trypsin 3,3’-[3,5-difluoro-4-methyl-2, 6-pyridinediylbis(oxy)]bis(benzenecarboximidamide) (ZK-805623) Complex (1999) doi 10.2210/pdb1QB6/pdb
PDB ID: 1QB9 Citation: Whitlow, M. Bovine Trypsin 7-[[2-[[1-(1-iminoethyl)piperidin-4-YL]oxy]-9H-carbozol-9-YL] methyl]naphthalene-2-carboximidamid (ZK-806450) Complex (1999) doi 10.2210/pdb1QB9/pdb
PDB ID: 1QBN Citation: Whitlow, M. Bovine Trypsin 2-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5-dihydro-1H-imidazol-2-yl)phenoxy]pyridine-4-carboxylic Acid (ZK-806688) Complex (1999) doi 10.2210/pdb1QBN/pdb
PDB ID: 1QBO Citation: Whitlow, M. Bovine Trypsin 7-[[6-[[1-(1-iminoethyl)piperidin-4-YL]oxy]-2-methyl-benzimidazol-1-YL]methyl]naphthalene-2-carboximidamid ZK-806711 Inhibitor Complex (1999) doi 10.2210/pdb1QBO/pdb
PDB ID: 1TNI Citation: Kurinov, I., Harrison, R.W. Prediction of Novel Serine Protease Inhibitors (1994) doi 10.2210/pdb1TNI/pdb
Estrogen antagonist receptor:
PDB ID: 3ERT Citation: Shiau, A.K., Barstad, D., Loria, P.M., Cheng, L., Kushner, P.J., Agard, D.A., Greene, G.L. Human Estrogen Receptor Alpha Ligand-Binding Domain in Complex with 4-Hydroxytamoxifen. (1999) doi 10.2210/pdb3ERT/pdb
Pierotti-1976
Pierotti, R.A.
A Scaled Particle Theory of Aqueous and Nonaqueous Solutions.
Chem. Rev 1976, 76 (6), 717–726.
DOI: 10.1021/cr60304a002
Reid-2014
Reid, R.; Yau, M.; Singh, R.; Hamidon, J.; Lim, J.; Stoermer, M.; Fairlie, D.
Potent Heterocyclic Ligands for Human Complement C3a Receptor.
J. Med. Chem. 2014, 57 (20), 8459–8470.
DOI: 10.1021/jm500956p
Rizzo-2006
Rizzo, R.C.; Aynechi, T.; Case, D.A.; Kuntz, I.D.
Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions.
J. Chem. Theory Comput. 2006, 2 (1), 128–139.
DOI: 10.1021/ct050097l
Rossi-2007
Rossi, K.A.; Weigelt, C.A.; Nayeem, A.; Krystek, S.R., Jr.
Loopholes and Missing Links in Protein Modeling.
Protein Sci. 2007, 16 (9), 1999–2012.
DOI: 10.1110/ps.072887807
Seidler-2003
Seidler, J.; McGovern, S.L.; Doman, T.N.; Shoichet, B.K.
Identification and Prediction of Promiscuous Aggregating Inhibitors among Known Drugs.
J. Med. Chem. 2003, 46 (21), 4477–4486.
DOI: 10.1021/jm030191r
Shannon-1949
Shannon, C.E.; Weaver, W.
The Mathematical Theory of Communication; University of Illinois Press, 1949.
ISBN 0252725484
Sharp-1991a
Sharp, K.A.; Nicholls, A.; Friedman, R.; Honig, B.
Extracting Hydrophobic Free Energies from Experimental Data: Relationship to Protein Folding and Theoretical Models.
Biochemistry 1991, 30 (40), 9686–9697.
DOI: 10.1021/bi00104a017
Sharp-1991b
Sharp, K.A.; Nicholls, A.; Fine, R.F.; Honig, B.
Reconciling the Magnitude of the Microscopic and Macroscopic Hydrophobic Effects.
Science 1991, 252 (5002), 106–109.
DOI: 10.1126/science.2011744
Sheridan-2002
Sheridan, R.P.
The Most Common Chemical Replacements in Drug-Like Compounds.
J. Chem. Inf. Comput. Sci. 2002, 42 (1), 103–108.
DOI: 10.1021/ci0100806
Spellmeyer-1997
Spellmeyer, D.C.; Wong, A.K.; Bower, M.J.; Blaney, J.M.
Conformational Analysis using Distance Geometry Methods.
J. Mol. Graphics Modell. 1997, 15 (1), 18–36.
DOI: 10.1016/s1093-3263(97)00014-4
Stahl-2001
Stahl, M.T.
You Want Conformers? I’ll Give You Conformers!
2nd Annual OpenEye Customers, Users, and Programmers Meeting, Santa Fe, NM, 2001.
Stahl-2002
Stahl, M.T.
Omega, AESOP, and Other Cautionary Tales of Naming Programs.
3rd Annual OpenEye Customers, Users, and Programmers Meeting, Santa Fe, NM, 2002.
Sykes-2008
Sykes, M.J.; McKinnon, R.A.; Miners, J.O.
Prediction of Metabolism by Cytochrome P450 2C9: Alignment and Docking Studies of a Validated Database of Substrates.
J. Med. Chem. 2008, 51 (4), 780–791.
DOI: 10.1021/jm7009793
Tolman-1949
Tolman, R.C.
The Effect of Droplet Size on Surface Tension.
J. Chem. Phys. 1949, 17 (3), 333–337.
DOI: 10.1063/1.1747247
Truchon-2009
Truchon, J.-F.; Nicholls, A.; Grant, J.A.; Iftimie, R.I.; Roux B.; Bayly, C.I.
Using Electronic Polarization from the Internal Continuum (EPIC) for Intermolecular Interactions.
J. Comput. Chem. 2009, 31 (4), 811–824.
DOI: 10.1002/jcc.21369
Tu-2012
Tu, M.; Rai, B.; Mathiowetz, A.; Didiuk, M.; Pfefferkorn, J.; Guzman-Perez, A.; Benbow, J.; Guimarães, C.; Mente, S.; Hayward, M.; Liras, S.
Exploring Aromatic Chemical Space with NEAT: Novel and Electronically Equivalent Aromatic Template.
J. Chem. Inf. Model. 2012, 52 (5), 1114–1123.
DOI: 10.1021/ci300031s
Tuccinardi-2010
Tuccinardi, T.; Botta, M.; Giordano, A.; Martinelli, A.
Protein Kinases: Docking and Homology Modeling Reliability.
J. Chem. Inf. Model. 2010, 50 (8), 1432–1441.
DOI: 10.1021/ci100161z
Ujváry-2003
Ujváry, I.; Györffy, W; Lopata, A.
Fragment-Based Drug Design using Stereoisomers. A Case Study of Analogues of the Phenol Group in the Bioster Database.
Acta Pharm. Hung. 2003, 73 (3), 163–169.
PMID: 15112439
Vagin-2004
Vagin, A.A.; Steiner, R.A.; Lebedev, A.A.; Potterton, L.; McNicholas, S.; Long, F.; Murshudov, G.N.
REFMAC5 Dictionary: Organization of Prior Chemical Knowledge and Guidelines for its Use.
Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, D60 (12), 2184–2195.
DOI: 10.1107/s0907444904023510
Veber-2002
Veber, D.F.; Johnson, S.R.; Cheng, H.-Y.; Smith, B.R.; Ward, K.W.; Kopple, K.D.
Molecular Properties that Influence the Oral Bioavailability of Drug Candidates.
J. Med. Chem. 2002, 45 (12), 2615–2623.
DOI: 10.1021/jm020017n
Verkhivker-2000
Verkhivker, G.M.; Bouzida, D.; Gehlhaar, D.K.; Rejto, P.A.; Arthurs, S.; Colson, A.B.; Freer, S.T.; Larson, V.; Luty, B.A.; Marrone, T.; et al.
Deciphering Common Failures in Molecular Docking of Ligand-Protein Complexes.
J. Comput.-Aided Mol. Des. 2000, 14 (8), 731–751.
DOI: 10.1023/a:1008158231558
Verloop-1987
Verloop, A.
The STERIMOL Approach to Drug Design, Marcel Dekker, New York, 1987.
Vidal-2005
Vidal, D.; Thormann, M.; Pons, M.
LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities.
J. Chem. Inf. Model. 2005, 45 (2), 386–393.
DOI: 10.1021/ci0496797
Virtanen-2010
Virtanen, S.I; Pentikäinen, O.T.
Efficient Virtual Screening using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site.
J. Chem. Inf. Model. 2010, 50 (6), 1005–1011.
DOI: 10.1021/ci100121c
Wang-J-2000
Wang, J.; Cieplak, P.; Kollman, P.A.
How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules?
J. Comput. Chem. 2000, 21 (12), 1049–1074.
DOI: 10.1002/1096-987x(200009)21:12<1049::aid-jcc3>3.0.co;2-f
Wang-R-1997
Wang, R.; Ying, F.; Lai, L.
A New Atom-Additive Method for Calculating Partition Coefficients.
J. Chem. Inf. Comput. Sci. 1997, 37 (3), 615–621.
DOI: 10.1021/ci960169p
Ward-2012
Ward, R.A.; Brassington, C.; Breeze, A.L.; Caputo, A.; Critchlow, S.; Davies, G.; Goodwin, L.; Hassall, G.; Greenwood, R.; Holdgate, G.A.; et al.
Design and Synthesis of Novel Lactate Dehydrogenase A Inhibitors by Fragment-Based Lead Generation.
J. Med. Chem. 2012, 55 (7), 3285–3306.
DOI: 10.1021/jm201734r
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.; et al.
A Critical Assessment of Docking Programs and Scoring Functions.
J. Med. Chem. 2006, 49 (12), 5912–5931.
DOI: 10.1021/jm050362n
Warren-2012
Warren, G.L.; Do, T.D.; Kelley, B.P.; Nicholls, A.; Warren, S.D.
Essential Considerations for Using Protein–Ligand Structures in Drug Discovery.
Drug Discov. Today 2012, 17 (23–24), 1270–1281.
DOI: 10.1016/j.drudis.2012.06.011
Watson-2001
Watson, P.; Willett, P.; Gillet, V.J.; Verdonk, M.L.
Calculating the Knowledge-Based Similarity of Functional Groups Using Crystallographic Data.
J. Comput.-Aided Mol. Des. 2001, 15, 835–857.
DOI: 10.1023/a:1013115500749
Watts-2014
Watts, K.S.; Dalal, P.; Tebben, A.J.; Cheney, D.L.; Shelley, J.C.
Macrocycle Conformational Sampling with MacroModel.
J. Chem. Inf. Model. 2014, 54 (10), 2680–2696.
DOI: 10.1021/ci5001696
Wikipedia-pValue
P-value. Wikipedia.
https://en.wikipedia.org/w/index.php?title=P-value&oldid=1142130724 (accessed May 2011).
Wlodek-2006
Wlodek, S.; Skillman, A.G.; Nicholls, A.
Automated Ligand Placement and Refinement with a Combined Force Field and Shape Potential.
Acta Crystallogr., Sect. D: Struct. Biol. 2006, 62 (7), 741–749.
DOI: 10.1107/s0907444906016076
Wlodek-2010
Wlodek, S.; Skillman, A.G.; Nicholls, A.
Ligand Entropy in Gas-Phase, Upon Solvation and Protein Complexation. Fast Estimation with Quasi-Newton Hessian.
J. Chem. Theory Comput. 2010, 6 (7), 2140–2152.
DOI: 10.1021/ct100095p
Yalkowsky-1980
Yalkowsky, S.H.; Valvani, S.C.
Solubility and Partitioning I: Solubility of Nonelectrolytes in Water.
J. Pharm. Sci. 1980, 69 (8), 912–922.
DOI: 10.1002/jps.2600690814