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FRED Publications

Featured Publications

M. McGann, "FRED Pose Prediction and Virtual Screening Accuracy", J. Chem. Inf. Model., 2011, 51 (3), pp 578-596

S.L. Swann, S.P. Brown, S.W. Muchmore, H. Patel, P. Merta, J. Locklear and P.J. Hajduk, "A Unified, Probabilistic Framework for Structure- and Ligand-Based Virtual Screening", J. Med. Chem., 2011, 54 (5), pp 1223-1232

T. Tuccinardi, M. Botta, A. Giordano, and A. Martinelli, "Protein Kinases: Docking and Homology Modeling Reliability", J. Chem. Inf. Model., 2010, 50(6), 1432-1440.

A.J.S. Knox, T. Price, M. Pawlak, G. Golfis, C.T. Flood, D. Fayne, D.C. Williams, M.J. Meegan and D.G. Lloyd, "Integration of Ligand and Structure-Based Virtual Screening for the Identification of the First Dual Targeting Agent for Heat Shock Protein 90 (Hsp90) and Tubulin", J. Med. Chem., 2009, 52 (8), pp 2177-2180

G.B. McGaughey, R.P. Sheridan, C.I. Bayly, J.C. Culberson, C. Kreatsolas, S. Lindsley, V. Maiorov, J.-F. Truchon and W.D. Cornell, "Comparison of Topological, Shape, and Docking Methods in Virtual Screening", J. Chem. Inf. Model., 2007, 47 (4), pp 1504-1519

M.R. McGann, H.R. Almond, A. Nicholls, J.A. Grant and F.K. Brown, "Gaussian docking functions", Biopolymers, 2003, 68 (1), pp 76-90

Publications by Date

M. McGann, "FRED Pose Prediction and Virtual Screening Accuracy", J. Chem. Inf. Model., 2011, 51 (3), pp 578-596

S.L. Swann, S.P. Brown, S.W. Muchmore, H. Patel, P. Merta, J. Locklear and P.J. Hajduk, "A Unified, Probabilistic Framework for Structure- and Ligand-Based Virtual Screening", J. Med. Chem., 2011, 54 (5), pp 1223-1232

A.J.S. Knox, T. Price, M. Pawlak, G. Golfis, C.T. Flood, D. Fayne, D.C. Williams, M.J. Meegan and D.G. Lloyd, "Integration of Ligand and Structure-Based Virtual Screening for the Identification of the First Dual Targeting Agent for Heat Shock Protein 90 (Hsp90) and Tubulin", J. Med. Chem., 2009, 52 (8), pp 2177-2180

R.P. Sheridan, "Alternative Global Goodness Metrics and Sensitivity Analysis: Heuristics to Check the Robustness of Conclusions from Studies Comparing Virtual Screening Methods", J. Chem. Inf. Model., 2008, 48 (2), pp 426-433

J.J. Sutherland, R.K. Nandigam, J.A. Erickson and M. Vieth, "Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy", J. Chem. Inf. Model., 2007, 47 (6), pp 2293-2302

G.B. McGaughey, R.P. Sheridan, C.I. Bayly, J.C. Culberson, C. Kreatsolas, S. Lindsley, V. Maiorov, J.-F. Truchon and W.D. Cornell, "Comparison of Topological, Shape, and Docking Methods in Virtual Screening", J. Chem. Inf. Model., 2007, 47 (4), pp 1504-1519

A.J.S. Knox, M.J. Meegan, G. Carta and D.G. Lloyd, "Considerations in Compound Database Preparation - “Hidden” Impact on Virtual Screening Results", J. Chem. Inf. Model., 2005, 45 (6), pp 1908-1919

G.L. Warren, C.W. Andrews, A.-M. Cappeli, B. Clarke, J. LaLonde, M.H. Lambert, M. Lindval, N. Nevins, S.F. Semus, S. Senger, G. Tedesco, I.D. Wall, J.M. Woolven, C.E. Peishoff and M.S. Head, "A Critical Assessment of Docking Programs and Scoring Functions", J. Med Chem., 2006, 49 (20), pp 5912-5931

E. Kellenberger, J. Rodrigo, P. Muller, and D. Rognan, "Comparative Evaluation of Eight Docking Tools for Docking and Virtual Screening Accuracy", Proteins: Structure, Function, and Bioinformatics, 2004, 57 (2), pp 225-242

T. Schulz-Gasch and M. Stahl, "Binding site characteristics in structure-based virtual screening: evaluation of current docking tools", J. Mol. Model., 2003, 9 (1), pp 47-57

M.R. McGann, H.R. Almond, A. Nicholls, J.A. Grant and F.K. Brown, "Gaussian docking functions", Biopolymers, 2003, 68 (1), pp 76-90

Bibliography & Related Publications

G.P.A. Vigers and J.P. Rizzi, "Multiple Active Site Corrections for Docking and Virtual Screening", J. Med. Chem., 2004, 47 (1), pp 80-89

M. Stahl and M. Rarey, "Detailed Analysis of Scoring Functions for Virtual Screening", J. Med. Chem., 2001, 44 (7), pp 1035-1042

C.A. Baxter, C.W. Murray, D.E. Clark, D.R. Westhead and M.D. Eldridge, "Flexible docking using tabu search and an empirical estimate of binding affinity", Proteins: Structure, Function, and Bioinformatics, 1998, 33 (3), pp 367-382

M.D. Eldridge, C.W. Murray, T.R. Auton, G.V. Paolini and R.P. Mee, "Empirical scoring functions: I. the development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes", J. Comp. Aided Mol. Des., 1997, 11 (5), pp 425-445

D.K. Gehlhaar, G.M. Verkhivker, P.A. Rejto, C.J. Sherman, D.R. Fogel, L.J. Fogel and S.T. Freer, "Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming", Chemistry & Biology, 1995, 2 (5), pp 317-324