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ROCS Publications

Featured Publications

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

S.W. Muchmore, D.A. Debe, J.T. Metz, S.P. Brown, Y.C. Martin and P.J. Hajduk, "Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping", J. Chem. Inf. Model., 2008, 48 (5), pp 941-948

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

Publications by Date

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, G. Ortore, M.A. Santos, S.M. Marques, E. Nuti, A. Rossello and A. Martinelli, "Multitemplate Alignment Method for the Development of a Reliable 3D-QSAR Model for the Analysis of MMP3 Inhibitors", J. Chem. Inf. Model., 2009, 49 (7), pp 1715–1724

J. Oyarzabai, T. Howe, J. Alcazar, J.I. Andres, R.M. Alvarez, F. Dautzenberg, L. Iturrino, S. Martinez and L. Van der Linden, "Novel Approach for Chemotype Hopping Based on Annotated Databases of Chemically Feasible Fragments and a Prospective Case Study: New Melanin Concentrating Hormone Antagonists", J. Med. Chem., 2009, 52 (7) pp 2076-2089

E. Naylor, A. Arredouani, S.R. Vasudevan, A.M. Lewis, R. Parkesh, A. Mizote, D. Rosen, J.M. Thomas, M. Izumi, A. Ganesan, A. Galione and G.C. Churchill, "Identification of a chemical probe for NAADP by virtual screening", Nature Chemical Biology, 2009, 5, pp 220-226

G. Tresadern, D. Bemporad and T. Howe, "A comparison of ligand based virtual screening methods and application to corticotropin releasing factor 1 receptor", J. Mol. Graph. and Model., 2009, 27 (8), pp 860-870

R.K. Nandigam, D.A. Evans, J.A. Erickson, S. Kim and J.J. Sutherland, "Predicting the Accuracy of Ligand Overlay Methods with Random Forest Models", J. Chem. Inf. Model., 2008, 48 (12), pp 2386-2394

J. Venhorst, S. Nunez, J.W. Terpstra and C.G. Kruse, "Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction Fingerprints", J. Med. Chem., 2008, 51 (11), pp 3222-3229

S.W. Muchmore, D.A. Debe, J.T. Metz, S.P. Brown, Y.C. Martin and P.J. Hajduk, "Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping", J. Chem. Inf. Model., 2008, 48 (5), pp 941-948

K. Moffat, V.J. Gillet, M. Whittle, G. Bravi and A.R. Leach, "A Comparison of Field-Based Similarity Searching Methods: CatShape, FBSS, and ROCS", J. Chem. Inf. Model., 2008, 48 (4), pp 719-729

H.S. Lee, J. Choi, I. Kufareva, R. Abagyan, A. Filikov, Y. Yang and S. Yoon, "Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods", J. Chem. Inf. Model., 2008, 48 (3), pp 489-497

V.I. Perez-Nueno, D.W. Ritchie, O. Rabal, R. Pascual, J.I. Borrell and J. Teixido, "Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape Matching and Ligand-Receptor Docking", J. Chem. Inf. Model., 2008, 48 (3), pp 509-533

R.P. Sheridan, G.B. McGaughey and W.D. Cornell, "Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results", J. Comp. Aided Mol. Des., 2008, 22 (3-4), pp 257-265

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

R.F. Freitas, T.I. Oprea and C.A. Montanari, "2D QSAR and similarity studies on cruzain inhibitors aimed at improving selectivity over cathepsin L", Bioorganic & Medicinal Chemistry, 2008, 16 (2), pp 838-853

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

J. Bostrom, K. Berggren, T. Elebring, P.J. Greasley and M. Wilstermann, "Scaffold hopping, synthesis and structure–activity relationships of 5,6-diaryl-pyrazine-2-amide derivatives: A novel series of CB1 receptor antagonists", Bioorganic & Medicinal Chemistry, 2007, 15 (12), pp 4077-4084

P.C.D. Hawkins, A.G. Skillman and A. Nicholls, "Comparison of Shape-Matching and Docking as Virtual Screening Tools", J. Med. Chem., 2007, 50 (1), pp 74-82

S.W. Muchmore, A.J. Souers and I. Akritopoulou-Zanze, "The Use of Three-Dimensional Shape and Electrostatic Similarity Searching in the Identification of a Melanin-Concentrating Hormone Receptor 1 Antagonist", Chemical Biology & Drug Design, 2006, 67 (2), pp 174-176

H. Chen, P.D. Lyne, F. Giordanetto, T. Lovell and J. Li, "On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors", J. Chem. Inf. Model., 2006, 46 (1), pp 401-415

J.A. Haigh, B.T. Pickup, J.A. Grant and A. Nicholls, "Small Molecule Shape-Fingerprints", J. Chem. Inf. Model., 2005, 45 (3), pp 673-684

T.S. Rush III, J.A. Grant, L. Mosyak and A. Nicholls, "A Shape-Based 3-D Scaffold Hopping Method and Its Application to a Bacterial Protein−Protein Interaction", J. Med. Chem., 2005, 48 (5), pp 1489-1495

A. Nicholls, N.E. MacCuish and J.D. MacCuish, "Variable selection and model validation of 2D and 3D molecular descriptors", J. Comp. Aided Mol. Des., 2004, 18 (7), pp 451-474

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", J. Comp. Chem., 1996, 14, pp 1653-1666

Bibliography & Related Publications

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", J. Comp. Chem., 1996, 14, pp 1653-1666