List of selected ROCS publications

  • 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, Journal of Computational Chemistry, Vol. 17, pp 1653-1666, 1996.

  • Nicholls, A., MacCuish, N.E., MacCuish, J.D., Variable Selection and Model Validation of 2D and 3D Molecular Descriptors, Journal of Computer-Aided Molecular Design, Vol. 18(7), pp 451-474, 2004.

  • Rush, T.S., Grant, J.A., Mosyak, L., Nicholls, A., A Shape-Based 3-D Scaffold Hopping Method and its Application to a Bacterial Protein-Protein Interaction, Journal of Medicinal Chemistry, Vol. 48, pp. 1489-1495, 2005.

  • Haigh, J.A.; Pickup, B.T., Grant, J.A. and Nicholls, A., Small Molecule Shape-Fingerprints, Journal of Chemical Information and Modeling, Vol. 45(3), pp. 673-684, 2005.

  • Chen, H., Lyne, P.D., Giordanetto, F., Lovell, T. and Li, J., On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors, Journal of Chemical Information and Modeling, Vol. 46, pp. 401-415, 2006.

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

  • Hawkins, P.C.D.; Skillman, A.G. and Nicholls, A., Comparison of Shape-Matching and Docking as Virtual Screening Tools, Journal of Medicinal Chemistry, Vol. 50, pp. 74-82, 2007.

  • 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., Comparison of Topological, Shape, and Docking Methods in Virtual Screening, Journal of Chemical Information and Modeling, Vol. 47, pp. 1504-1519, 2007.

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

  • Sutherland, J.J., Nandigam, R.K.; Erickson, J.A. and Vieth, M., Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy, Journal of Chemical Information and Modeling, Vol. 47, pp. 2293-2302, 2007.

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

  • Sheridan, R.P., McGaughey, G.B. and Cornell, W.D., Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results, Journal of Computer-Aided Molecular Design, Vol. 22, pp. 257-265, 2008.

  • Venhorst, J., Nunez, S., Terpstra, J.W. and Kruse, C.G., Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction Fingerprints, Journal of Medicinal Chemistry, Vol. 51(11), pp. 3222-3229, 2008.

  • Nandigam, R.K., Evans, D.A., Erickson, J.A., Kim, S. and Sutherland, J.J., Predicting the Accuracy of Ligand Overlay Methods with Random Forest Models, Journal of Chemical Information and Modeling, Vol. 48, pp. 2386-2394, 2008.

  • Sheridan, R.P., Alternative Global Goodness Metrics and Sensitivity Analysis: Heuristics to Check the Robustness of Conclusions from Studies Comparing Virtual Screening Methods, Journal of Chemical Information and Modeling, Vol. 48, pp. 426-433, 2008.

  • Lee, H.S., Choi, J., Kufareva, I., Abagyan, R., Filikov, A., Yang, Y. and Yoon, S. Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods, Journal of Chemical Information and Modeling, Vol. 48, pp. 489-497, 2008.

  • Pérez-Nueno, V.I., Ritchie, D.W., Rabal, O., Pascual, R., Borrell, J.I. and Teixido, J., 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, Journal of Chemical Information and Modeling, Vol. 48, pp. 509-533, 2008.

  • Moffat, K., Gillet, V.J., Whittle, M., Bravi, G. and Leach, A.R., A Comparison of Field-Based Similarity Searching Methods: CatShape, FBSS, and ROCS, Journal of Chemical Information and Modeling Vol. 48, pp. 719-729, 2008.

  • Muchmore, S.W., Debe, D.A., Metz, J.T., Brown, S.P., Martin, Y.C. and Hajduk, P.J., Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping, Journal of Chemical Information and Modeling, Vol. 48, pp. 491-498, 2008.

  • Naylor, E., Arredouani, A., Vasudevan, S.R., Lewis, A.M., Parkesh, R., Mizote, A., Rosen, D., Thomas, J.M., Izumi, M., Ganesan, A., Galione, A. and Churchill, G.C., Identification of a Chemical Probe for NAADP by Virtual Screening, Nature Chemical Biology, Vol. 5, pp. 220-226, 2009.

  • Oyarzabal, J., Howe, T., Alcazar, J., Andres, J.I., Alvarez, R.M., Dautzenberg, F., Iturrino, L., Martınez, S. and Van der Linden, I., Novel Approach for Chemotype Hopping Based on Annotated Databases of Chemically Feasible Fragments and a Prospective Case Study: New Melanin Concentrating Hormone Antagonists, Journal of Medicinal Chemistry, Vol. 52, pp. 2076-2089, 2009.

  • Tresadern, G., Bemporad, D. and Howe, T., A Comparison of Ligand Based Virtual Screening Methods and Application to Corticotropin Releasing Factor 1 Receptor, Journal of Molecular Graphics and Modelling, Vol. 27, pp. 860-870, 2009.

  • Tuccinardi, T., Ortors, G., Santos, M.A., Warques, S.M., Nuti, E., Rossello, A. and Martinelli, A., Multitemplate Alignment Method for the Development of a Reliable 3D-QSAR Model for the Analysis of MMP3 Inhibitors, Journal of Chemical Information and Modeling, Vol. 49(7), pp. 1715-1724, 2009.

  • Nicholls, A., McGaughey, G.B., Sheridan, R.P., Good, A.C., Warren, G., Mathieu, M., Muchmore, S.W., Brown, S.P., Grant, J.A., Haigh, J.A., Nevins, N., Jain, A.N. and Kelley, B., Molecular Shape and Medicinal Chemistry: A Perspective, Journal of Medicinal Chemistry, Vol. 53(10), pp. 3862-3886, 2010.

  • Kruger, D.M. and Evers, A., Comparison of Structure- and Ligand-Based Virtual Screening Protocols Considering Hitlist Complementarity and Enrichment Factors, Chem. Med. Chem., Vol. 5, pp. 148-158, 2010.

  • Swann, S.L., Brown, S.P., Muchmore, S.W., Patel, H., Merta, P., Locklear, J. and Hajduk, P.J., A Unified Probabilistic Framework for Structure- and Ligand-Based Virtual Screening, Journal of Medicinal Chemistry, Vol. 54(5), pp. 1223-1232, 2011.