The image above is from Cleves and Jain (2006). It is a two-way hierarchical clustering of drugs and targets based on molecular similarity.

Cleves, A. E. and Jain, A. N. (2017). ForceGen 3D structure and conformer generation: From small lead-like molecules to macrocyclic drugs. Journal of Computer-Aided Molecular Design.

Cleves, A. E. and Jain, A. N. (2016). Extrapolative prediction using physically-based QSAR. Journal of Computer-Aided Molecular Design, 30(2), 127-152.

Cleves, A. E. and Jain, A. N. (2015). Knowledge-Guided Docking: Accurate Prospective Prediction of Bound Configurations of Novel Ligands using Surflex-Dock. Journal of Computer-Aided Molecular Design, 29(6), 485-509.

Cleves, A. E. and Jain, A. N. (2015). Chemical and Protein Structural Basis for Biological Crosstalk Between PPAR-alpha and COX Enzymes. Journal of Computer-Aided Molecular Design, 29(2),101-112.

Yera, E. R., Cleves, A. E., & Jain, A. N. (2014). Prediction of off-target drug effects through data fusion. In Pacific Symposium on Biocomputing (Vol. 19, pp. 160-171).

Varela, R., Cleves, A. E., Spitzer, R., and Jain, A. N. (2013). A structure-guided approach for protein pocket modeling and affinity prediction. Journal of Computer-Aided Molecular Design, 27(11), 917-934.

Spitzer, R., Cleves, A. E., Varela, R., and Jain, A. N. (2013). Protein function annotation by local binding site surface similarity. Proteins: Structure, Function, and Bioinformatics.

Varela, R., Walters, W. P., Goldman, B. B., and Jain, A. N. (2012). Iterative Refinement of a Binding Pocket Model: Active Computational Steering of Lead Optimization. Journal of Medicinal Chemistry, 55(20), 8926-8942.

Spitzer, R., and Jain, A.N. (2012). Surflex-Dock: Docking Benchmarks and Real-World Application. J Computer-Aided Molecular Design, 26: 687-699.

Jain, A.N., and Cleves, A.C. (2012). Does Your Model Weigh the Same as a Duck? J Computer-Aided Molecular Design, 26, 57-67.

Yera, E.R., Cleves, A.E., and Jain, A.N. (2011) Chemical Structural Novelty: On-Targets and Off-Targets. J Med Chem, 64: 6771-6785.

Spitzer, R., Cleves, A.E., and Jain, A.N. (2011) Surface-Based Protein Binding Pocket Similarity. Proteins, 79: 2746-2763.

Jain, A.N. (2010). QMOD: Physically Meaningful QSAR. J Computer-Aided Molecular Design, 24, 865-878.

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. (2010) Molecular Shape and Medicinal Chemistry: A Perspective. J Med Chem, 53: 3862-3886.

Langham, J.J., Cleves, A.E., Spitzer, R., Kirshner, D., and Jain, A.N. (2009). Physical Binding Pocket Induction for Affinity Prediction. J Med Chem, 52: 6107-6125.

Jain, A.N. (2009). Effects of Protein Conformation in Docking: Improved Pose Prediction Through Protein Pocket Adaptation. J Computer-Aided Molecular Design, 23: 355-374

Cleves, A.E. and Jain, A.N. (2008). Effects of Inductive Bias on Computational Evaluations of Ligand-Based Modeling and on Drug Discovery. J Computer-Aided Molecular Design, 22, 147-159

Jain, A.N. (2008). Bias, Reporting, and Sharing: Computational Evaluations of Docking Methods. J Computer-Aided Molecular Design, 22, 201-212.

Pham, T. A. and Jain, A.N. (2008). Customizing Scoring Functions for Docking. J Computer-Aided Molecular Design, 22, 269-286.

Langham, J.J. and Jain, A.N. (2008). Accurate and Interpretable Computational Modeling of Chemical Mutagenicity. J Chem Inf Model, 48, 1833-1839.

Jain, A.N. (2007). Surflex-Dock 2.1: Robust Performance from Ligand Energetic Modeling, Ring Flexibility, and Knowledge-Based Search. J Computer-Aided Molecular Design, 21, 281-306.

Cleves, A. E. and Jain, A.N. (2006). Robust Ligand-Based Modeling of the Biological Targets of Known Drugs. J Med Chem, 49, 2921-2938

Hon, L.S. and Jain, A.N. (2006). A Deterministic Motif Finding Algorithm With Application to the Human Genome. Bioinformatics, 22, 1047-1054.

Pham, T. A. and Jain, A.N. (2006). Parameter Estimation for Scoring Protein-Ligand Interactions using Negative Training Data. J Med Chem, 49, 5856-5868.

Bussey, K.J., Chin, K., Lababidi, S., Reimers, M., Reinhold, W.C., Kuo, W.-L., Gwadry, F., Kouros-Mehr, H., Fridlyand, J., Jain, A.N., Collins, C., Nishizuka, S., Tonon, G., Roschke, A., Gehlhaus, K., Kirsch, I., Scudiero, D.A., Gray, J. and Weinstein, J.N. (2006). Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 Cell Line Panel. Molecular Cancer Therapeutics, 5, 853-867

Novak, B.A. and Jain, A.N. (2006). Pathway Recognition and Augmentation by Computational Analysis of Microarray Expression Data. Bioinformatics, 22, 233-241.

Kingsley, C. B., Kuo, W-L., Polikoff, D., Berchuck, A., Gray, J.W., and Jain, A.N. (2006). Magellan: A Web Based System for the Integrated Analysis of Heterogeneous Biological Data and Annotations; Application to DNA Copy Number and Expression Data in Ovarian Cancer. Cancer Informatics, 1, 10-21.

Snijders, A.M., Nowak, N.J., Huey, B., Fridlyand, J., Law, S., Conroy, J., Tokuyasu, T., Demir, K., Chiu, R., Mao, J.H., Jain, A.N., Jones, S.J., Balmain, A., Pinkel, D. and Albertson, D.G. (2005). Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res, 15, 302-311.

Mehta, K.R., Nakao, K., Zuraek, M.B., Ruan, D.T., Bergsland, E.K., Venook, A.P., Moore, D.H., Tokuyasu, T.A., Jain, A.N., Warren, R.S., Terdiman, J.P. and Waldman, F.M. (2005). Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer. Clin Cancer Res, 11, 1791-1797.

Jain, A.N. (2004). Virtual Screening in Lead Discovery and Optimization. Curr Op Drug Discovery & Dev, 7, 396-403.

Jain, A.N. (2004). Ligand-Based Structural Hypotheses for Virtual Screening. J Med Chem. 47, 947-961.

Nakao, K., Mehta, K.R., Fridlyand, J., Moore, D.H., Jain, A.N., Lafuente, A., Wiencke, J.W., Terdiman, J.P. and Waldman, F.M. (2004). High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis, 25, 1345-1357.

Paris, P.L., Andaya, A., Fridlyand, J., Jain, A.N., Weinberg, V., Kowbel, D., Brebner, J.H., Simko, J., Watson, J.E., Volik, S., Albertson, D.G., Pinkel, D., Alers, J.C., Van Der Kwast, T.H., Vissers, K.J., Schroder, F.H., Wildhagen, M.F., Febbo, P.G., Chinnaiyan, A.M., Pienta, K.J., Carroll, P.R., Rubin, M.A., Collins, C. and Van Dekken, H. (2004). Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet, 13, 1303-1313.

Rosen, D.G., Wang, L., Jain, A.N., Lu, K.H., Luo, R.Z., Yu, Y., Liu, J. and Bast, R.C., Jr. (2004). Expression of the tumor suppressor gene ARHI in epithelial ovarian cancer is associated with increased expression of p21WAF1/CIP1 and prolonged progression-free survival. Clin Cancer Res, 10, 6559-6566.

Fridlyand, J., Snijders, A.M., Pinkel, D., Albertson, D.G., and Jain, A.N. (2004). Hidden Markov Model Analysis of Array CGH Data. Journal of Multivariate Analysis 90, 132-153.

Hackett, C. S., Hodgson, J. G., Law, M. E., Fridlyand, J., Osoegawa, K., de Jong, P. J., Nowak, N. J., Pinkel, D., Albertson, D. G., Jain, A. N., Jenkins, R., Gray, J. W., Weiss, W. A. (2003) Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors. Cancer Res. 63, 5266-5273.

Maldonado, J. L., Fridlyand, J., Patel, H., Jain, A. N., Busam, K., Kageshita, T., Ono, T., Albertson, D. G., Pinkel, D., Bastian, B. C. (2003) Determinants of BRAF mutations in primary melanomas. J Natl Cancer Inst. 95, 1878-1890.

Hon, L.S. and Jain, A.N. (2003). Compositional Structure of Repetitive Elements is Quantitatively Related to Co-Expression of Gene Pairs. Journal of Molecular Biology, 332, 305-310.

Jain, A.N. (2003). Surflex: Fully Automatic Flexible Molecular Docking using a Molecular Similarity-Based Search Engine. J Med Chem. 46, 499-511.

Snijders, A.M., Fridlyand, J., Mans, D.A., Segraves, R., Jain, A.N., Pinkel, D. & Albertson, D.G. (2003). Shaping of tumor and drug-resistant genomes by instability and selection. Oncogene 22, 4370-9.

Snijders, A.M., Nowee, M.E., Fridlyand, J., Piek, J.M., Dorsman, J.C., Jain, A.N., Pinkel, D., Van Diest, P.J., Verheijen, R.H. & Albertson, D.G. (2003). Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in Fallopian tube carcinoma. Oncogene 22, 4281-6.

Veltman, J.A., Fridlyand, J., Pejavar, S., Olshen, A.B., Korkola, J.E., Devries, S., Carroll, P., Kuo, W.L., Pinkel, D., Albertson, D., Cordon-Cardo, C., Jain, A.N. & Waldman, F.M. (2003). Array-based Comparative Genomic Hybridization for Genome-Wide Screening of DNA Copy Number in Bladder Tumors. Cancer Res 63, 2872-80.

Paris, P.L., Albertson, D.G., Alers, J.C., Andaya, A., Carroll, P., Fridlyand, J., Jain, A.N., Kamkar, S., Kowbel, D., Krijtenburg, P.J., Pinkel, D., Schroder, F.H., Vissers, K.J., Watson, V.J., Wildhagen, M.F., Collins, C. & Van Dekken, H. (2003). High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Am J Pathol 162, 763-70.

Wilhelm, M., Veltman, J.A., Olshen, A.B., Jain, A.N., Moore, D.H., Presti, J.C., Jr., Kovacs, G. & Waldman, F.M. (2002). Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res 62, 957-60.

Olshen, A.B. & Jain, A.N. (2002). Deriving quantitative conclusions from microarray expression data. Bioinformatics 18, 961-70.

Massion, P.P., Kuo, W.L., Stokoe, D., Olshen, A.B., Treseler, P.A., Chin, K., Chen, C., Polikoff, D., Jain, A.N., Pinkel, D., Albertson, D.G., Jablons, D.M. & Gray, J.W. (2002). Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: Implications of the phosphatidylinositol 3-kinase pathway. Cancer Res 62, 3636-40.

Jain, A.N., Tokuyasu, T.A., Snijders, A.M., Segraves, R., Albertson, D.G. & Pinkel, D. (2002). Fully automatic quantification of microarray image data. Genome Res 12, 325-32.

Snijders, A.M., Nowak, N., Segraves, R., Blackwood, S., Brown, N., Conroy, J., Hamilton, G., Hindle, A.K., Huey, B., Kimura, K., Law, S., Myambo, K., Palmer, J., Ylstra, B., Yue, J.P., Gray, J.W., Jain, A.N., Pinkel, D. & Albertson, D.G. (2001). Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29, 263-4.

Perkins, E., Sun, D., Nguyen, A., Tulac, S., Francesco, M., Tavana, H., Nguyen, H., Tugendreich, S., Barthmaier, P., Couto, J., Yeh, E., Thode, S., Jarnagin, K., Jain, A.N., Morgans, D. & Melese, T. (2001). Novel inhibitors of poly(ADP-ribose) polymerase/PARP1 and PARP2 identified using a cell-based screen in yeast. Cancer Res 61, 4175-83.

Jain, A.N., Chin, K., Borresen-Dale, A.L., Erikstein, B.K., Eynstein Lonning, P., Kaaresen, R. & Gray, J.W. (2001). Quantitative analysis of chromosomal CGH in human breast tumors associates copy number abnormalities with p53 status and patient survival. Proc Natl Acad Sci U S A 98, 7952-7.

Jain, A.N. (2000). Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition. J Comput Aided Mol Des 14, 199-213.

Mount, J., Ruppert, J., Welch, W. & Jain, A.N. (1999). IcePick: A flexible surface-based system for molecular diversity. J Med Chem 42, 60-6.

Ghuloum, A.M., Sage, C.R. & Jain, A.N. (1999). Molecular hashkeys: A novel method for molecular characterization and its application for predicting important pharmaceutical properties of molecules. J Med Chem 42, 1739-48.

Ruppert, J., Welch, W. & Jain, A.N. (1997). Automatic identification and representation of protein binding sites for molecular docking. Protein Sci 6, 524-33.

Welch, W., Ruppert, J. & Jain, A.N. (1996). Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol 3, 449-62.

Jain, A.N. (1996). Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities. J Comput Aided Mol Des 10, 427-40.

Jain, A.N., Harris, N.L. & Park, J.Y. (1995). Quantitative binding site model generation: compass applied to multiple chemotypes targeting the 5-HT1A receptor. J Med Chem 38, 1295-308.

Jain, A.N., Koile, K. & Chapman, D. (1994). Compass: Predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark. J Med Chem 37, 2315-27.

Jain, A.N., Dietterich, T.G., Lathrop, R.H., Chapman, D., Critchlow, R.E., Jr., Bauer, B.E., Webster, T.A. & Lozano-Perez, T. (1994). A shape-based machine learning tool for drug design. J Comput Aided Mol Des 8, 635-52.

Dietterich, T.G., Jain, A.N., Lathrop, R.L. & Lozano-Perez, T. (1994). A Comparison of Dynamic Reposing and Tangent Distance for Drug Activity Prediction. In Advances in Neural Information Processing Systems 6 (ed. J. D. Cowan, G. Tesauro and J. Alspector). Morgan Kaufmann, San Mateo, CA.

Kramer, A.P. & Jain, A.N. (1993). Neural Network Clutter Rejection for FLIR ATR. In Proceedings of SPIE 1993.

Waibel, A., Jain, A.N., Mcnair, A.E., Tebelskis, J., Hauptmann, A. & Saito, H. (1992). JANUS: Speech-to-Speech Translation Using Connectionist and Non-Connectionist Techniques. In Advances in Neural Information Processing Systems 4 (ed. J. E. Moody, S. J. Hanson and R. P. Lippmann). Morgan Kaufmann, San Mateo, CA.

Jain, A.N., Waibel, A. & Touretzky, D.S. (1992). PARSEC: A Structured Connectionist Parsing System for Spoken Language. In Proceedings of the 1992 International Conference on Acoustics, Speech, and Signal Processing. IEEE.

Jain, A.N. (1992). Generalization Performance in PARSEC-A Structured Connectionist Parsing Architecture. In Advances in Neural Information Processing Systems 4 (ed. J. E. Moody, S. J. Hanson and R. P. Lippmann). Morgan Kaufmann, San Mateo, CA.

Waibel, A.H., Jain, A.N., Mcnair, A.E., Saito, H., Hauptmann, A.G. & Tebelskis, J. (1991). JANUS: A Speech-to-Speech Translation System Using Connectionist and Symbolic Processing Strategies. In Proceedings of the 1991 International Conference on Acoustics, Speech, and Signal Processing. IEEE.

Jain, A.N., Mcnair, A.E., Waibel, A.H., Saito, H., Hauptmann, A.G. & Tebelskis, J. (1991). Connectionist and Symbolic Processing in Speech-to-Speech Translation: The JANUS System. In Proceedings of the MT Summit III Machine Translation Conference.

Jain, A.N. (1991). Parsing Complex Sentences with Structured Connectionist Networks. Neural Computation 3, 110-20.

Jain, A.N. & Waibel, A.H. (1990). Robust Connectionist Parsing of Spoken Language. In Proceedings of the 1990 International Conference on Acoustics, Speech, and Signal Processing, pp. 593-96. IEEE.

Jain, A.N. & Waibel, A.H. (1990). Incremental Parsing by Modular Recurrent Connectionist Networks. In Advances in Neural Information Processing Systems 2 (ed. D. S. Touretzky), pp. 364-71. Morgan Kaufmann, San Mateo, CA.

Jain, A.N. & Krig, D. (1986). A Robust Hough Technique for Machine Vision. In Proceedings of Vision '86. Society of Manufacturing Engineers, Dearborn, MI.



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