Zap and Poisson-Boltzman Electrostatics

• "A Smooth Permittivity Function for Poisson-Boltzmann Solvation Methods," J. A. Grant, B. T. Pickup, A. Nicholls, J. Comp. Chem, 22 (2001) 608-640.
• "Validation of Poisson-Boltzmann Electrostatic Potential Fields in 3D QSAR: A CoMFA Study on Multiple Datasets," G. E Kellogg, S. Phatak, A. Nicholls, J. A. Grant, QSAR & Comb. Sci., 22 (2003) 959-64.
• "Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method," Ninad V. Prabhu, Peijuan Zhu, Kim A. Sharp, J. Comp. Chem., 25, 16 (2004) 2049-2064.
• "High-Throughput Calculation of Protein-Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing," Scott P. Brown and Steven W. Muchmore, J. Chem. Inf. Model, 46 (2006), pp. 999-1005.

ROCS, Shape Theory and Applications

• "A fast method of molecular shape comparison. A simple application of a Gaussian description of molecular shape," J. A. Grant, M. A. Gallardo, B. T. Pickup, J. Comp. Chem, 17, (1996) 1653-1666.
• "A Shape-Based 3-D Scaffold Hopping Method and its Application to a Bacterial Protein-Protein Interaction," Rush, T.S., Grant, J.A., Mosyak, L., Nicholls, A., J. Med. Chem. 48 (2005) 1489-1495.
• "Small Molecule Shape-Fingerprints," J. A. Haigh, B. T. Pickup, J. A. Grant, and A. Nicholls, J. Chem. Inf. Model., 45(3) (2005) 673-684.
• "Variable Selection and Model Validation of 2D and 3D Molecular Descriptors," A. Nicholls, N.E. MacCuish, J.D. MacCuish, J. Comp.-Aided Mol. Des. 18: 451-474, (2004).
• "On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors", Hongming Chen, et al., J. Chem. Inf. Model, 2006, 46, 401-415.
• "Comparison of Shape-Matching and Docking as Virtual Screening Tools, " Paul C. D. Hawkins, A. Geoffrey Skillman, and Anthony Nicholls, J. Med. Chem., 50 (1), 74 -82, 2007.
• " Comparison of Topological, Shape, and Docking Methods in Virtual Screening," McGaughey, G.B., Sheridan, R.P., Bayly, C.I., Culberson, J.C., Kreatsoulas, C., Lindsley, S., Maiorov, V., Truchon, J.-F., and Cornell, W.D., J. Chem. Inf. Model., 2007.
• " Scaffold hopping, synthesis and structure-activity relationships of 5,6-diaryl-pyrazine-2-amide derivatives: A novel series of CB1 receptor antagonists", Jonas Boström, Kristina Berggren, Thomas Elebring, Peter J. Greasleya and Michael Wilstermanna, Bioorganic & Medicinal Chemistry, 15 (2007) pp 4077-4084.

Omega and Conformational Analysis

• "Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools," J. Boström, J. Comp.-Aid. Mol. Design 15 (2001) 1137.
• "Assessing the performance of OMEGA with respect to retrieving bioactive conformations," J. Boström, J. R. Greenwood, J. Gottfries, J. Mol. Graphics and Mod. 21 (2003) 449-462.
• "Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding," E. Perola and P.S. Charifson, J. Med. Chem. 47 (2004) 2499-2510.
• "CORES: An Automated Method for Generating Three-Dimensional Models of Protein/Ligand Complexes," B.J. Hare, W.P. Walters, P.R. Caron, G.W. Bemis, J. Med. Chem. 47 (2004) 4731-4740.
• "Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations," Johannes Kirchmair, Gerhard Wolber, Christian Laggner, and Thierry Langer, J. Chem. Info. Model, 46(4), pp. 1848-1861, 2006.

Fred and Docking

• "Binding site characteristics in structure-based virtual screening: evaluation of current docking tools," T. Schultz-Gasch, M. Stahl, J. Mol. Model. 9 (2003) 47-57.
• "Gaussian Docking Functions," M. McGann, H. Almond, A. Nicholls, J. A. Grant, F. K. Brown. Biopolymers, 68 (2003) pp.76-90, Wiley Periodicals.
• "Comparative Evaluation of Eight Docking Tools for Docking and Virtual Screening Accuracy," Esther Kellenberger, Jordi Rodrigo, Pascal Muller, and Didier Rognan. Proteins: Structure, Function, and Bioinformatics 57:225-242 (2004) .
• "A Critical Assessment of Docking Programs and Scoring Functions" [PDF], G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, and M. S. Head, J. Med. Chem., 49 (20), 5912-5931, 2006.
• " Comparison of Topological, Shape, and Docking Methods in Virtual Screening," McGaughey, G.B., Sheridan, R.P., Bayly, C.I., Culberson, J.C., Kreatsoulas, C., Lindsley, S., Maiorov, V., Truchon, J.-F., and Cornell, W.D., J. Chem. Inf. Model., 2007.

• (MASC) "Multiple active site corrections for docking and virtual screening," G.P. Vigers, J.P. Rizzi, J. Med. Chem. 47 (2004) 80-9.
• (PLP scoring function) "Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming," D.K. Gehlhaar, G.M. Verkhivker, P.A. Rejto, C.J. Sherman, D.B. Fogel, L.J. Fogel and S.T. Freer, Chemistry & Biology 2 (1995) 317-324.
• (Chemscore) "Empirical scoring functions: I. the development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes," M. Eldridge, C. Murray, T. Auton, G. Paolini, R. Mee, J. Comp.-Aided Mol. Des. 11 (1997) 425-445.
• (Chemscore) "Flexible docking using TABU search and an empirical estimate of binding affinity," C.A. Baxter, C.W. Murray, D.E. Clark, D.R. Westhead, M.D. Eldridge, Proteins 33, (1997) 367-382.
• (Screenscore) "Detailed Analysis of Scoring Functions for Virtual Screening," M. Stahl, M. Rarey, J. Med. Chem, 44 (2001) 1035-1042.

OEChem and Chemoinformatics

• "ZINC - A Free Database of Commercially Available Compounds for Virtual Screening," Irwin, J. J.; Shoichet, B. K.; J. Chem. Inf. Model 45(1) (2005) 177-182.
• "Database Clustering with a Combination of Fingerprint and Maximum Common Substructure Methods," M. Stahl and H. Mauser, J. Chem. Inf. Model 45(3) (2005) p542-548.
• "Lingos, Finite State Machines, and Fast Similarity Searching," J. A. Grant, J. A. Haigh, B. T. Pickup, A. Nicholls, and R. A. Sayle, J. Chem. Inf. Model 46(5) (2006) p1912-1918.

Afitt and Crystallography

• "Automated Ligand Placement and Refinement with a Combined Force Field and Shape Potential," S. Wlodek, A.G. Skillman and A. Nicholls, Acta Crystallographica D, D62, pp. 741-749 (2006). (Also available from Acta Cryst.)

Other

• " A simple formula for dielectric polarisation energies: The Sheffield Solvation Model," Chemical Physics Letters, Volume 441, Issues 1-3, 13 June 2007, pp 163-166, J.A. Grant, B.T. Pickup, M.J. Sykes, C.A. Kitchen and A. Nicholls.
• " How to do an evaluation: pitfalls and traps," Journal of Computer-Aided Molecular Design, 23 January 2008, Paul C. D. Hawkins, Gregory L. Warren, A. Geoffrey Skillman, and Anthony Nicholls.