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.
[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