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Ajay N. Jain - Publications

Affiliations: 
University of California, San Francisco, San Francisco, CA 
Area:
Molecular Biology, Computer Science
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47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Jain AN, Cleves AE, Brueckner AC, Lesburg CA, Deng Q, Sherer EC, Reibarkh M. XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-Ray Electron Density Maps. Journal of Medicinal Chemistry. PMID 32877178 DOI: 10.1021/Acs.Jmedchem.0C01373  0.304
2020 Cleves AE, Jain AN. Structure-Based and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding-Pocket. Journal of Chemical Information and Modeling. PMID 32271577 DOI: 10.1021/Acs.Jcim.0C00115  0.393
2019 Cleves AE, Johnson SR, Jain AN. Electrostatic-field and surface-shape similarity for virtual screening and pose prediction. Journal of Computer-Aided Molecular Design. PMID 31650386 DOI: 10.1007/S10822-019-00236-6  0.436
2019 Jain AN, Cleves AE, Gao Q, Wang X, Liu Y, Sherer EC, Reibarkh MY. Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen. Journal of Computer-Aided Molecular Design. PMID 31054028 DOI: 10.1007/S10822-019-00203-1  0.338
2018 Cleves AE, Jain AN. Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose. Journal of Computer-Aided Molecular Design. PMID 29934750 DOI: 10.1007/S10822-018-0126-X  0.44
2017 Cleves AE, Jain AN. ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs. Journal of Computer-Aided Molecular Design. PMID 28289981 DOI: 10.1007/S10822-017-0015-8  0.412
2016 Cleves AE, Jain AN. Extrapolative prediction using physically-based QSAR. Journal of Computer-Aided Molecular Design. PMID 26860112 DOI: 10.1007/S10822-016-9896-1  0.458
2015 Singh N, Jain N, Kumar R, Jain A, Singh NK, Rai V. A comparative method for protein extraction and 2-D gel electrophoresis from different tissues of Cajanus cajan. Frontiers in Plant Science. 6: 606. PMID 26300903 DOI: 10.3389/Fpls.2015.00606  0.3
2015 Cleves AE, Jain AN. Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock. Journal of Computer-Aided Molecular Design. 29: 485-509. PMID 25940276 DOI: 10.1007/S10822-015-9846-3  0.447
2015 Cleves AE, Jain AN. Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes. Journal of Computer-Aided Molecular Design. 29: 101-12. PMID 25428568 DOI: 10.1007/S10822-014-9815-2  0.441
2014 Yera ER, Cleves AE, Jain AN. Prediction of off-target drug effects through data fusion. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 160-71. PMID 24297543  0.76
2014 Spitzer R, Cleves AE, Varela R, Jain AN. Protein function annotation by local binding site surface similarity. Proteins. 82: 679-94. PMID 24166661 DOI: 10.1002/Prot.24450  0.766
2014 Steudle A, Varela R, Jain AN. Surflex-QMOD: physically meaningful QSAR Journal of Cheminformatics. 6. DOI: 10.1186/1758-2946-6-S1-P55  0.461
2013 Varela R, Cleves AE, Spitzer R, Jain AN. A structure-guided approach for protein pocket modeling and affinity prediction. Journal of Computer-Aided Molecular Design. 27: 917-34. PMID 24214361 DOI: 10.1007/S10822-013-9688-9  0.775
2012 Varela R, Walters WP, Goldman BB, Jain AN. Iterative refinement of a binding pocket model: active computational steering of lead optimization. Journal of Medicinal Chemistry. 55: 8926-42. PMID 23046104 DOI: 10.1021/Jm301210J  0.355
2012 Spitzer R, Jain AN. Surflex-Dock: Docking benchmarks and real-world application. Journal of Computer-Aided Molecular Design. 26: 687-99. PMID 22569590 DOI: 10.1007/S10822-011-9533-Y  0.776
2012 Jain AN, Cleves AE. Does your model weigh the same as a duck? Journal of Computer-Aided Molecular Design. 26: 57-67. PMID 22187141 DOI: 10.1007/S10822-011-9530-1  0.313
2011 Yera ER, Cleves AE, Jain AN. Chemical structural novelty: on-targets and off-targets. Journal of Medicinal Chemistry. 54: 6771-85. PMID 21916467 DOI: 10.1021/Jm200666A  0.751
2011 Spitzer R, Cleves AE, Jain AN. Surface-based protein binding pocket similarity. Proteins. 79: 2746-63. PMID 21769944 DOI: 10.1002/Prot.23103  0.773
2010 Jain AN. QMOD: physically meaningful QSAR. Journal of Computer-Aided Molecular Design. 24: 865-78. PMID 20721601 DOI: 10.1007/S10822-010-9379-8  0.476
2010 Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, Nevins N, Jain AN, Kelley B. Molecular shape and medicinal chemistry: a perspective. Journal of Medicinal Chemistry. 53: 3862-86. PMID 20158188 DOI: 10.1021/Jm900818S  0.343
2009 Langham JJ, Cleves AE, Spitzer R, Kirshner D, Jain AN. Physical binding pocket induction for affinity prediction. Journal of Medicinal Chemistry. 52: 6107-25. PMID 19754201 DOI: 10.1021/Jm901096Y  0.781
2009 Jain AN. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. Journal of Computer-Aided Molecular Design. 23: 355-74. PMID 19340588 DOI: 10.1007/S10822-009-9266-3  0.437
2008 Langham JJ, Jain AN. Accurate and interpretable computational modeling of chemical mutagenicity. Journal of Chemical Information and Modeling. 48: 1833-9. PMID 18771257 DOI: 10.1021/Ci800094A  0.35
2008 Jain AN, Nicholls A. Recommendations for evaluation of computational methods. Journal of Computer-Aided Molecular Design. 22: 133-9. PMID 18338228 DOI: 10.1007/S10822-008-9196-5  0.425
2008 Pham TA, Jain AN. Customizing scoring functions for docking. Journal of Computer-Aided Molecular Design. 22: 269-86. PMID 18273558 DOI: 10.1007/S10822-008-9174-Y  0.433
2008 Jain AN. Bias, reporting, and sharing: computational evaluations of docking methods. Journal of Computer-Aided Molecular Design. 22: 201-12. PMID 18075713 DOI: 10.1007/S10822-007-9151-X  0.405
2008 Cleves AE, Jain AN. Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery. Journal of Computer-Aided Molecular Design. 22: 147-59. PMID 18074107 DOI: 10.1007/S10822-007-9150-Y  0.419
2007 Jain AN. Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. Journal of Computer-Aided Molecular Design. 21: 281-306. PMID 17387436 DOI: 10.1007/S10822-007-9114-2  0.416
2006 Kingsley CB, Kuo WL, Polikoff D, Berchuck A, Gray JW, Jain AN. 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. 2: 10-21. PMID 19458754 DOI: 10.1177/117693510600200019  0.761
2006 Jain AN. Scoring functions for protein-ligand docking. Current Protein & Peptide Science. 7: 407-20. PMID 17073693 DOI: 10.2174/138920306778559395  0.394
2006 Pham TA, Jain AN. Parameter estimation for scoring protein-ligand interactions using negative training data. Journal of Medicinal Chemistry. 49: 5856-68. PMID 17004701 DOI: 10.1021/Jm050040J  0.413
2006 Cleves AE, Jain AN. Robust ligand-based modeling of the biological targets of known drugs. Journal of Medicinal Chemistry. 49: 2921-38. PMID 16686535 DOI: 10.1021/Jm051139T  0.343
2006 Hon LS, Jain AN. A deterministic motif finding algorithm with application to the human genome. Bioinformatics (Oxford, England). 22: 1047-54. PMID 16455748 DOI: 10.1093/Bioinformatics/Btl037  0.742
2006 Novak BA, Jain AN. Pathway recognition and augmentation by computational analysis of microarray expression data. Bioinformatics (Oxford, England). 22: 233-41. PMID 16278238 DOI: 10.1093/Bioinformatics/Bti764  0.672
2004 Jain AN. Ligand-based structural hypotheses for virtual screening. Journal of Medicinal Chemistry. 47: 947-61. PMID 14761196 DOI: 10.1021/Jm030520F  0.452
2003 Hon LS, Jain AN. Compositional structure of repetitive elements is quantitatively related to co-expression of gene pairs. Journal of Molecular Biology. 332: 305-10. PMID 12948482 DOI: 10.1016/S0022-2836(03)00926-4  0.72
2003 Jain AN. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. Journal of Medicinal Chemistry. 46: 499-511. PMID 12570372 DOI: 10.1021/Jm020406H  0.396
2000 Jain AN. Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition. Journal of Computer-Aided Molecular Design. 14: 199-213. PMID 10721506 DOI: 10.1023/A:1008100132405  0.416
1999 Ghuloum AM, Sage CR, Jain AN. Molecular hashkeys: a novel method for molecular characterization and its application for predicting important pharmaceutical properties of molecules. Journal of Medicinal Chemistry. 42: 1739-48. PMID 10346926 DOI: 10.1021/Jm980527A  0.363
1999 Mount J, Ruppert J, Welch W, Jain AN. IcePick: a flexible surface-based system for molecular diversity. Journal of Medicinal Chemistry. 42: 60-6. PMID 9888833 DOI: 10.1021/Jm970775R  0.329
1997 Ruppert J, Welch W, Jain AN. Automatic identification and representation of protein binding sites for molecular docking. Protein Science : a Publication of the Protein Society. 6: 524-33. PMID 9070435 DOI: 10.1002/Pro.5560060302  0.447
1996 Jain AN. Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities Journal of Computer-Aided Molecular Design. 10: 427-440. PMID 8951652 DOI: 10.1007/Bf00124474  0.437
1996 Welch W, Ruppert J, Jain AN. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chemistry & Biology. 3: 449-62. PMID 8807875 DOI: 10.1016/S1074-5521(96)90093-9  0.441
1995 Jain AN, Harris NL, Park JY. Quantitative binding site model generation: compass applied to multiple chemotypes targeting the 5-HT1A receptor. Journal of Medicinal Chemistry. 38: 1295-308. PMID 7731016 DOI: 10.1021/Jm00008A008  0.398
1994 Jain AN, Koile K, Chapman D. Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark. Journal of Medicinal Chemistry. 37: 2315-27. PMID 8057280 DOI: 10.1021/Jm00041A010  0.39
1994 Jain AN, Dietterich TG, Lathrop RH, Chapman D, Critchlow RE, Bauer BE, Webster TA, Lozano-Perez T. Compass: A shape-based machine learning tool for drug design Journal of Computer-Aided Molecular Design. 8: 635-652. PMID 7738601 DOI: 10.1007/Bf00124012  0.373
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