Selected ROCS Publications

Numerous journal articles have been published about ROCS through the years. Included here are some of the more impactful papers. They are arranged in chronological order, beginning with the seminal work on Gaussians by Grant, Gallardo, and Pickup.

  • 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

  • Nicholls, A.; MacCuish, N.E.; MacCuish, J.D. Variable Selection and Model Validation of 2D and 3D Molecular Descriptors. J. Comput.-Aided Mol. Des. 2004, 18 (7), 451–474. DOI: 10.1007/s10822-004-5202-8

  • Rush, T.S.; Grant, J.A.; Mosyak, L.; Nicholls, A. A Shape-Based 3D Scaffold Hopping Method and Its Application to a Bacterial Protein–Protein Interaction. J. Med. Chem. 2005, 48 (5), 1489–1495. DOI: 10.1021/jm040163o

  • Haigh, J.A.; Pickup, B.T.; Grant, J.A.; Nicholls, A. Small Molecule Shape-Fingerprints. J. Chem. Inf. Model. 2005, 45 (3), 673-684. DOI: 10.1021/ci049651v

  • Chen, H.; Lyne, P.D.; Giordanetto, F.; Lovell, T.; Li, J. On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors. J. Chem. Inf. Model. 2006, 46 (1), 401–415. DOI: 10.1021/ci0503255

  • Muchmore, S.W.; Souers, A.J.; Akritopoulou-Zanze, I. The Use of Three-Dimensional Shape and Electrostatic Similarity Searching in the Identification of a Melanin-Concentrating Hormone Receptor 1 Antagonist. Chem. Biol. Drug Des. 2006, 67 (2), 174–176. DOI: 10.1111/j.1747-0285.2006.00341.x

  • Hawkins, P.C.D.; Skillman, A.G.; Nicholls, A. Comparison of Shape-Matching and Docking as Virtual Screening Tools. J. Med. Chem. 2007, 50 (1), 74–82. DOI: 10.1021/jm0603365

  • McGaughey, G.B.; Sheridan, R.P.; Bayly, C.I.; Culberson, J.C.; Kreatsoulas, C.; Lindsley, S.; Maiorov, V.; Truchon, J.-F.; Cornell, W.D. Comparison of Topological, Shape, and Docking Methods in Virtual Screening. J. Chem. Inf. Model. 2007, 47 (4), 1504–1519. DOI: 10.1021/ci700052x

  • Boström, J.; Berggren, K., Elebring, T.; Greasley, P.J.; Wilstermann, M. Scaffold Hopping, Synthesis and Structure–Activity Relationships of 5,6-diaryl-pyrazine-2-amide Derivatives: A Novel Series of CB1 Receptor Antagonists. Bioorg. Med. Chem. 2007, 15 (12), 4077–4084. DOI: 10.1016/j.bmc.2007.03.075

  • Sutherland, J.J.; Nandigam, R.K.; Erickson, J.A.; Vieth, M. Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy. J. Chem. Inf. Model. 2007, 47 (6), 2293–2302. DOI: 10.1021/ci700253h

  • Freitas, R.F.; Oprea, T.I.; Montanari, C.A. 2D QSAR and Similarity Studies on Cruzain Inhibitors Aimed at Improving Selectivity over cathepsin L. Bioorg. Med. Chem. 2008, 16 (2), 838–853. DOI: 10.1016/j.bmc.2007.10.048

  • Sheridan, R.P.; McGaughey, G.B.; Cornell, W.D. Multiple Protein Structures and Multiple Ligands: Effects on the Apparent Goodness of Virtual Screening Results. J. Comput.-Aided Mol. Des. 2008, 22, 257–265. DOI: 10.1007/s10822-008-9168-9

  • Venhorst, J.; Núñez, S.; Terpstra, J.W.; Kruse, C.G. Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction Fingerprints. J. Med. Chem. 2008, 51 (11), 3222–3229. DOI: 10.1021/jm8001058

  • Nandigam, R.K.; Evans, D.A.; Erickson, J.A.; Kim, S.; Sutherland, J.J. Predicting the Accuracy of Ligand Overlay Methods with Random Forest Models. J. Chem. Inf. Model. 2008, 48 (12), 2386–2394. DOI: 10.1021/ci800216f

  • Sheridan, R.P. 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), 426–433. DOI: 10.1021/ci700380x

  • Lee, H.S.; Choi, J.; Kufareva, I.; Abagyan, R.; Filikov, A.; Yang, Y.; Yoon, S. Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods. J. Chem. Inf. Model. 2008, 48 (3), 489–497. DOI: 10.1021/ci700376c

  • Pérez-Nueno, V.I.; Ritchie, D.W.; Rabal, O.; Pascual, R.; Borrell, J.I.; Teixidó, 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, J. Chem. Inf. Model. 2008, 48 (3), 509–533. DOI: 10.1021/ci700415g

  • Moffat, K.; Gillet, V.J.; Whittle, M.; Bravi, G.; Leach, A.R. A Comparison of Field-Based Similarity Searching Methods: CatShape, FBSS, and ROCS. J. Chem. Inf. Model. 2008, 48 (4), 719–729. DOI: 10.1021/ci700130j

  • 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

  • Naylor, E.; Arredouani, A.; Vasudevan, S.R.; et al. Identification of a Chemical Probe for NAADP by Virtual Screening. Nat. Chem. Biol. 2009, 5, 220–226. DOI: 10.1038/nchembio.150

  • Oyarzabal, J.; Howe, T.; Alcazar, J.; Andres, J.I.; Alvarez, R.M.; Dautzenberg, F.; Iturrino, L.; Martınez, S.; 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. J. Med. Chem. 2009, 52 (7), 2076–2089. DOI: 10.1021/jm8016199

  • Tresadern, G.; Bemporad, D.; Howe, T. A Comparison of Ligand Based Virtual Screening Methods and Application to Corticotropin Releasing Factor 1 Receptor. J. Mol. Graphics Modell. 2009, 27 (8), 860–870. DOI: 10.1016/j.jmgm.2009.01.003

  • Tuccinardi, T.; Ortors, G.; Santos, M.A.; Marques, S.M.; Nuti, E.; Rossello, A.; Martinelli, A. 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), 1715–1724. DOI: 10.1021/ci900118v

  • 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.; Kelley, B. Molecular Shape and Medicinal Chemistry: A Perspective. J. Med. Chem. 2010, 53 (10), 3862–3886. DOI: 10.1021/jm900818s

  • Krüger, D.M.; Evers, A. Comparison of Structure- and Ligand-Based Virtual Screening Protocols Considering Hitlist Complementarity and Enrichment Factors. ChemMedChem 2010, 5 (1), 148–158. DOI: 10.1002/cmdc.200900314

  • Swann, S.L.; Brown, S.P.; Muchmore, S.W.; Patel, H.; Merta, P.; Locklear, J.; Hajduk, P.J. A Unified Probabilistic Framework for Structure- and Ligand-Based Virtual Screening. J. Med. Chem. 2011, 54 (5), 1223–1232. DOI: 10.1021/jm1013677

  • Wollenhaupt, J.; Metz, A.; Barthel, T.; Lima, G.M.A.; Heine, A.; Mueller, U.; Klebe, G.; Weiss, M.S. F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening. Structure 2020, 28 (6), 694–706.e5. DOI: 10.1016/j.str.2020.04.019

  • Taylor, A.I.P.; Xu, Y.; Wilkinson, M.; Chakraborty, P.; Brinkworth, A.; Willis, L.F.; Zhuravleva, A.; Ranson, N.A.; Foster, R.; Radford, S.E. Kinetic Steering of Amyloid Formation and Polymorphism by Canagliflozin, a Type-2 Diabetes Drug. J. Am. Chem. Soc. 2025, 147 (14), 11859–11878. DOI: 10.1021/jacs.4c16743

  • Rossen, L.; Sirockin, F.; Schneider, N.; Grisoni, F. Scaffold Hopping with Generative Reinforcement Learning. J. Chem. Inf. Model. 2025, 65 (13), 6513–6525. DOI: 10.1021/acs.jcim.5c00029