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Ajay Jain, PhD

Title(s)Professor, HDF Comprehensive Cancer Ctr
SchoolSchool of Medicine
Address1450 Third St
San Francisco CA 94158
Phone415-502-7242
ORCID ORCID Icon0000-0003-4641-8501 Additional info
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    Collapse Overview 
    Collapse Overview
    Predictive computational modeling encompasses all of the work in the Jain Lab. This takes primary form in algorithmic approaches for drug discovery. The primary areas of research in the lab are: 1) methods for docking small molecules to proteins using empirically derived scoring functions, 2) methods for inducing the shape of a protein binding pocket given the structures and affinities of ligands that bind the pocket competitively, 3) generalized surface-based approaches to computing molecular similarity, both among small molecules and proteins, 4) approaches for modeling and prediction of polypharmacology based on molecular structure, and 5) applications of such methods for cancer drug discovery. All of the approaches share their roots in the use of sophisticated computational algorithms involving object representation, function optimization, and search.

    History
    Following a long period of applied research in defense applications and in speech understanding, Prof. Jain began a research career exclusively focused on issues in computational chemistry and computational biology. His foundational work in computer-aided drug design was done in industry, beginning with the Compass and Hammerhead techniques (see papers from 1994-1997). Compass involved a new representational scheme for capturing the 3D surface-properties of small molecules that made it possible to systematically address a previously unaddressed aspect in modeling the activity of small molecules: choice of the relative alignment and conformation (or pose) of competitive ligands including the detailed relationship of their hydrophobic shapes. A key insight, made with colleagues, was that the choice of pose should be directly governed by the function being used to predict binding affinity (essentially a direct analogy to physics where the lowest energy state is sought). The difficulty was that the function to predict activity was being induced at the same time as the pose choice. The Compass method overcame this problem, and was one of the foundational methods in establishing the field of multiple-instance learning, as it has come to be known within the Computer Science community. This work lead to the development of one of the first molecular docking programs described that addressed ligand conformational flexibility. The Hammerhead docking system built upon the molecular representations, multiple-instance approach, and search strategy developed for Compass.

    Advances in Molecular Docking and Ligand-Based Modeling
    Subsequent work built on the foundation laid by Compass and Hammerhead. These methods addressed problems in computation of molecular diversity and prediction of ADME properties (see papers from 1998-2000). Our most recent work in computational drug design (see the Surflex methodological papers from 2003 onward) is focused on pushing the frontiers of molecular docking and in constructing ligand-based models of protein active sites in cases where protein structure is unknown. The Surflex docking approach is unique, both with respect to scoring function and search methodology. Surflex-Dock is competitive with the best and most widely available methods in terms of docking accuracy and screening utility on publicly available benchmarks. We have recently made a substantial innovation to the multiple-instance parameter estimation process by generalizing our approach to now include negative training data. Putative inactive molecules have been added to a set of known active molecules in re-estimation of the scoring function for the Surflex docking method. We have continued our work in ligand-based modeling as well. The Surflex similarity method has been augmented, both in search strategy and in its objective function, to support the construction of ligand-based models of protein activity. The models are competitive with the best docking methods in terms of effectiveness in identifying novel ligands, generalizing remarkably well even across different chemical scaffolds. The Surflex QMOD approach takes QSAR to a new level, by transforming the problem into one of molecular docking. A protein binding site is induced given structure-activity data using the multiple-instance machine learning paradigm developed for Compass.

    Rational and Predictive Pharmacology
    Research within the lab has branched out to encompass larger biological scales, with studies that contemplate the multiple effects of small molecules in the whole organism. Our earliest work in drug discovery focused exclusively on the therapeutically desired target. At least as important are off-targets: those that are not intended to be modulated by a therapeutic but are affected at relevant drug concentrations. We are interested in building accurate predictive models for promiscuous bad-actor targets such as hERG and cytochrome-p450 enzymes. More broadly, we are interested in building models for multitudes of human targets in order to help guide the design and selection of compounds during preclinical research. This is challenging, both in terms of the stringency on model accuracy and also in terms of information curation regarding the multiple effects of existing therapeutics and those that have undergone clinical testing.

    Wet Applications
    The laboratory is purely a dry one. We rely upon our collaborators to test predictions made by our computational tools. In addition to the hundreds of laboratories that make use of our software, we have active collaborations with both academic and industrial partners. We are particularly interested in applications involving cancer.

    Collapse Research 
    Collapse Research Activities and Funding
    Binding-Site Modeling with Multiple-Instance Machine-Learning
    NIH/NIGMS R01GM101689Jan 1, 2013 - Mar 31, 2021
    Role: Principal Investigator
    Data-Driven Approaches for Molecular Docking
    NIH/NIGMS R01GM070481Jul 1, 2005 - Jun 30, 2014
    Role: Principal Investigator
    Cancer Center Support Grant
    NIH/NCI P30CA082103Aug 5, 1999 - Sep 29, 2012
    Role: Co-Investigator

    Collapse ORNG Applications 
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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket. J Chem Inf Model. 2020 Apr 21. Cleves AE, Jain AN. PMID: 32271577.
      View in: PubMed   Mentions:    Fields:    
    2. OsSQD1 at the crossroads of phosphate and sulfur metabolism affects plant morphology and lipid composition in response to phosphate deprivation. Plant Cell Environ. 2020 Jul; 43(7):1669-1690. Sun Y, Jain A, Xue Y, Wang X, Zhao G, Liu L, Hu Z, Hu S, Shen X, Liu X, Ai H, Xu G, Sun S. PMID: 32266981.
      View in: PubMed   Mentions:    Fields:    
    3. OsPDR2 mediates the regulation on the development response and maintenance of Pi homeostasis in rice. Plant Physiol Biochem. 2020 Apr; 149:1-10. Cao Y, Jain A, Ai H, Liu X, Wang X, Hu Z, Sun Y, Hu S, Shen X, Lan X, Xu G, Sun S. PMID: 32028088.
      View in: PubMed   Mentions:    Fields:    
    4. Electrostatic-field and surface-shape similarity for virtual screening and pose prediction. J Comput Aided Mol Des. 2019 10; 33(10):865-886. Cleves AE, Johnson SR, Jain AN. PMID: 31650386.
      View in: PubMed   Mentions:    Fields:    
    5. Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen. J Comput Aided Mol Des. 2019 06; 33(6):531-558. Jain AN, Cleves AE, Gao Q, Wang X, Liu Y, Sherer EC, Reibarkh MY. PMID: 31054028.
      View in: PubMed   Mentions:    Fields:    
    6. OsSIZ2 regulates nitrogen homeostasis and some of the reproductive traits in rice. J Plant Physiol. 2019 Jan; 232:51-60. Pei W, Jain A, Ai H, Liu X, Feng B, Wang X, Sun Y, Xu G, Sun S. PMID: 30530203.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    7. Angiography Alone Versus Angiography Plus Optical Coherence Tomography to Guide Percutaneous Coronary Intervention: Outcomes From the Pan-London PCI Cohort. JACC Cardiovasc Interv. 2018 07 23; 11(14):1313-1321. Jones DA, Rathod KS, Koganti S, Hamshere S, Astroulakis Z, Lim P, Sirker A, O'Mahony C, Jain AK, Knight CJ, Dalby MC, Malik IS, Mathur A, Rakhit R, Lockie T, Redwood S, MacCarthy PA, Desilva R, Weerackody R, Wragg A, Smith EJ, Bourantas CV. PMID: 30025725.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    8. Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose. J Comput Aided Mol Des. 2018 07; 32(7):731-757. Cleves AE, Jain AN. PMID: 29934750.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    9. Clinically Actionable Hypercholesterolemia and Hypertriglyceridemia in Children with Nonalcoholic Fatty Liver Disease. J Pediatr. 2018 07; 198:76-83.e2. Harlow KE, Africa JA, Wells A, Belt PH, Behling CA, Jain AK, Molleston JP, Newton KP, Rosenthal P, Vos MB, Xanthakos SA, Lavine JE, Schwimmer JB. PMID: 29661561.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    10. ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs. J Comput Aided Mol Des. 2017 May; 31(5):419-439. Cleves AE, Jain AN. PMID: 28289981.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    11. Antihypertensive Effects of a Central Arteriovenous Anastomosis Are Mediated Through Profound Reduction in Systemic Vascular Resistance. Circ Cardiovasc Interv. 2016 08; 9(8):e004012. Saxena M, Sobotka PA, Hamshere SM, Jain A, Mathur A, Knight C, Collier DJ, Lobo MD. PMID: 27512091.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    12. Extrapolative prediction using physically-based QSAR. J Comput Aided Mol Des. 2016 Feb; 30(2):127-52. Cleves AE, Jain AN. PMID: 26860112.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    13. Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock. J Comput Aided Mol Des. 2015 Jun; 29(6):485-509. Cleves AE, Jain AN. PMID: 25940276.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    14. Atypical risk factor profile and excellent long-term outcomes of young patients treated with primary percutaneous coronary intervention for ST-elevation myocardial infarction. Eur Heart J Acute Cardiovasc Care. 2016 Feb; 5(1):23-32. Rathod KS, Jones DA, Gallagher S, Rathod VS, Weerackody R, Jain AK, Mathur A, Mohiddin SA, Archbold RA, Wragg A, Knight CJ. PMID: 25589633.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    15. Chemical and protein structural basis for biological crosstalk between PPARa and COX enzymes. J Comput Aided Mol Des. 2015 Feb; 29(2):101-12. Cleves AE, Jain AN. PMID: 25428568.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    16. Prediction of off-target drug effects through data fusion. Pac Symp Biocomput. 2014; 160-71. Yera ER, Cleves AE, Jain AN. PMID: 24297543.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    17. Protein function annotation by local binding site surface similarity. Proteins. 2014 Apr; 82(4):679-94. Spitzer R, Cleves AE, Varela R, Jain AN. PMID: 24166661.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    18. A structure-guided approach for protein pocket modeling and affinity prediction. J Comput Aided Mol Des. 2013 Nov; 27(11):917-34. Varela R, Cleves AE, Spitzer R, Jain AN. PMID: 24214361.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    19. Tumour antigen targeted monoclonal antibodies incorporating a novel multimerisation domain significantly enhance antibody dependent cellular cytotoxicity against colon cancer. Eur J Cancer. 2013 Oct; 49(15):3344-52. Jain A, Poonia B, So EC, Vyzasatya R, Burch EE, Olsen HS, Mérigeon EY, Block DS, Zhang X, Schulze DH, Hanna NN, Twadell WS, Yfantis HG, Chan SL, Cai L, Strome SE. PMID: 23871153.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    20. Iterative refinement of a binding pocket model: active computational steering of lead optimization. J Med Chem. 2012 Oct 25; 55(20):8926-42. Varela R, Walters WP, Goldman BB, Jain AN. PMID: 23046104.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    21. Fully recombinant IgG2a Fc multimers (stradomers) effectively treat collagen-induced arthritis and prevent idiopathic thrombocytopenic purpura in mice. Arthritis Res Ther. 2012 Aug 20; 14(4):R192. Jain A, Olsen HS, Vyzasatya R, Burch E, Sakoda Y, Mérigeon EY, Cai L, Lu C, Tan M, Tamada K, Schulze D, Block DS, Strome SE. PMID: 22906120.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    22. Surflex-Dock: Docking benchmarks and real-world application. J Comput Aided Mol Des. 2012 Jun; 26(6):687-99. Spitzer R, Jain AN. PMID: 22569590.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    23. Successful recanalization of chronic total occlusions is associated with improved long-term survival. JACC Cardiovasc Interv. 2012 Apr; 5(4):380-8. Jones DA, Weerackody R, Rathod K, Behar J, Gallagher S, Knight CJ, Kapur A, Jain AK, Rothman MT, Thompson CA, Mathur A, Wragg A, Smith EJ. PMID: 22516393.
      View in: PubMed   Mentions: 28     Fields:    Translation:Humans
    24. Does your model weigh the same as a duck? J Comput Aided Mol Des. 2012 Jan; 26(1):57-67. Jain AN, Cleves AE. PMID: 22187141.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    25. Chemical structural novelty: on-targets and off-targets. J Med Chem. 2011 Oct 13; 54(19):6771-85. Yera ER, Cleves AE, Jain AN. PMID: 21916467.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    26. Surface-based protein binding pocket similarity. Proteins. 2011 Sep; 79(9):2746-63. Spitzer R, Cleves AE, Jain AN. PMID: 21769944.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    27. QMOD: physically meaningful QSAR. J Comput Aided Mol Des. 2010 Oct; 24(10):865-78. Jain AN. PMID: 20721601.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    28. Molecular shape and medicinal chemistry: a perspective. J Med Chem. 2010 May 27; 53(10):3862-86. 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. PMID: 20158188.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansCells
    29. Physical binding pocket induction for affinity prediction. J Med Chem. 2009 Oct 08; 52(19):6107-25. Langham JJ, Cleves AE, Spitzer R, Kirshner D, Jain AN. PMID: 19754201.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    30. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J Comput Aided Mol Des. 2009 Jun; 23(6):355-74. Jain AN. PMID: 19340588.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    31. Accurate and interpretable computational modeling of chemical mutagenicity. J Chem Inf Model. 2008 Sep; 48(9):1833-9. Langham JJ, Jain AN. PMID: 18771257.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    32. Recommendations for evaluation of computational methods. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):133-9. Jain AN, Nicholls A. PMID: 18338228.
      View in: PubMed   Mentions: 68     Fields:    Translation:HumansAnimals
    33. Customizing scoring functions for docking. J Comput Aided Mol Des. 2008 May; 22(5):269-86. Pham TA, Jain AN. PMID: 18273558.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    34. Bias, reporting, and sharing: computational evaluations of docking methods. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):201-12. Jain AN. PMID: 18075713.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    35. Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):147-59. Cleves AE, Jain AN. PMID: 18074107.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    36. Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J Comput Aided Mol Des. 2007 May; 21(5):281-306. Jain AN. PMID: 17387436.
      View in: PubMed   Mentions: 133     Fields:    
    37. 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 Inform. 2007 Feb 05; 2:10-21. Kingsley CB, Kuo WL, Polikoff D, Berchuck A, Gray JW, Jain AN. PMID: 19458754.
      View in: PubMed   Mentions:
    38. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006 Dec; 10(6):529-41. Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW. PMID: 17157792.
      View in: PubMed   Mentions: 495     Fields:    Translation:HumansCells
    39. Parameter estimation for scoring protein-ligand interactions using negative training data. J Med Chem. 2006 Oct 05; 49(20):5856-68. Pham TA, Jain AN. PMID: 17004701.
      View in: PubMed   Mentions: 50     Fields:    Translation:Cells
    40. Scoring functions for protein-ligand docking. Curr Protein Pept Sci. 2006 Oct; 7(5):407-20. Jain AN. PMID: 17073693.
      View in: PubMed   Mentions: 43     Fields:    Translation:AnimalsCells
    41. Robust ligand-based modeling of the biological targets of known drugs. J Med Chem. 2006 May 18; 49(10):2921-38. Cleves AE, Jain AN. PMID: 16686535.
      View in: PubMed   Mentions: 27     Fields:    
    42. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer. 2006 Apr 18; 6:96. Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG. PMID: 16620391.
      View in: PubMed   Mentions: 106     Fields:    Translation:HumansCells
    43. Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther. 2006 Apr; 5(4):853-67. Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F, Kouros-Mehr H, Fridlyand J, Jain A, Collins C, Nishizuka S, Tonon G, Roschke A, Gehlhaus K, Kirsch I, Scudiero DA, Gray JW, Weinstein JN. PMID: 16648555.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansCells
    44. A deterministic motif finding algorithm with application to the human genome. Bioinformatics. 2006 May 01; 22(9):1047-54. Hon LS, Jain AN. PMID: 16455748.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    45. Selective targeting of antitumor immune responses with engineered live-attenuated Listeria monocytogenes. Cancer Res. 2006 Jan 15; 66(2):1096-104. Yoshimura K, Jain A, Allen HE, Laird LS, Chia CY, Ravi S, Brockstedt DG, Giedlin MA, Bahjat KS, Leong ML, Slansky JE, Cook DN, Dubensky TW, Pardoll DM, Schulick RD. PMID: 16424046.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    46. Pathway recognition and augmentation by computational analysis of microarray expression data. Bioinformatics. 2006 Jan 15; 22(2):233-41. Novak BA, Jain AN. PMID: 16278238.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    47. Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer. Clin Cancer Res. 2005 Mar 01; 11(5):1791-7. Mehta KR, Nakao K, Zuraek MB, Ruan DT, Bergsland EK, Venook AP, Moore DH, Tokuyasu TA, Jain AN, Warren RS, Terdiman JP, Waldman FM. PMID: 15756001.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    48. Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res. 2005 Feb; 15(2):302-11. Snijders AM, Nowak NJ, Huey B, Fridlyand J, Law S, Conroy J, Tokuyasu T, Demir K, Chiu R, Mao JH, Jain AN, Jones SJ, Balmain A, Pinkel D, Albertson DG. PMID: 15687294.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    49. 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. 2004 Oct 01; 10(19):6559-66. Rosen DG, Wang L, Jain AN, Lu KH, Luo RZ, Yu Y, Liu J, Bast RC. PMID: 15475444.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    50. Virtual screening in lead discovery and optimization. Curr Opin Drug Discov Devel. 2004 Jul; 7(4):396-403. Jain AN. PMID: 15338948.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    51. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet. 2004 Jul 01; 13(13):1303-13. Paris PL, Andaya A, Fridlyand J, Jain AN, Weinberg V, Kowbel D, Brebner JH, Simko J, Watson JE, Volik S, Albertson DG, Pinkel D, Alers JC, van der Kwast TH, Vissers KJ, Schroder FH, Wildhagen MF, Febbo PG, Chinnaiyan AM, Pienta KJ, Carroll PR, Rubin MA, Collins C, van Dekken H. PMID: 15138198.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansCells
    52. High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis. 2004 Aug; 25(8):1345-57. Nakao K, Mehta KR, Fridlyand J, Moore DH, Jain AN, Lafuente A, Wiencke JW, Terdiman JP, Waldman FM. PMID: 15001537.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansCells
    53. Ligand-based structural hypotheses for virtual screening. J Med Chem. 2004 Feb 12; 47(4):947-61. Jain AN. PMID: 14761196.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    54. Determinants of BRAF mutations in primary melanomas. J Natl Cancer Inst. 2003 Dec 17; 95(24):1878-90. Maldonado JL, Fridlyand J, Patel H, Jain AN, Busam K, Kageshita T, Ono T, Albertson DG, Pinkel D, Bastian BC. PMID: 14679157.
      View in: PubMed   Mentions: 139     Fields:    Translation:Humans
    55. Compositional structure of repetitive elements is quantitatively related to co-expression of gene pairs. J Mol Biol. 2003 Sep 12; 332(2):305-10. Hon LS, Jain AN. PMID: 12948482.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    56. Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors. Cancer Res. 2003 Sep 01; 63(17):5266-73. Hackett CS, Hodgson JG, Law ME, Fridlyand J, Osoegawa K, de Jong PJ, Nowak NJ, Pinkel D, Albertson DG, Jain A, Jenkins R, Gray JW, Weiss WA. PMID: 14500357.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansAnimalsCells
    57. Shaping of tumor and drug-resistant genomes by instability and selection. Oncogene. 2003 Jul 10; 22(28):4370-9. Snijders AM, Fridlyand J, Mans DA, Segraves R, Jain AN, Pinkel D, Albertson DG. PMID: 12853973.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    58. Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma. Oncogene. 2003 Jul 03; 22(27):4281-6. Snijders AM, Nowee ME, Fridlyand J, Piek JM, Dorsman JC, Jain AN, Pinkel D, van Diest PJ, Verheijen RH, Albertson DG. PMID: 12833150.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    59. Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Res. 2003 Jun 01; 63(11):2872-80. Veltman JA, Fridlyand J, Pejavar S, Olshen AB, Korkola JE, DeVries S, Carroll P, Kuo WL, Pinkel D, Albertson D, Cordon-Cardo C, Jain AN, Waldman FM. PMID: 12782593.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansCells
    60. High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Am J Pathol. 2003 Mar; 162(3):763-70. Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg PJ, Pinkel D, Schröder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, Van Dekken H. PMID: 12598311.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    61. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem. 2003 Feb 13; 46(4):499-511. Jain AN. PMID: 12570372.
      View in: PubMed   Mentions: 252     Fields:    Translation:Cells
    62. Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway. Cancer Res. 2002 Jul 01; 62(13):3636-40. Massion PP, Kuo WL, Stokoe D, Olshen AB, Treseler PA, Chin K, Chen C, Polikoff D, Jain AN, Pinkel D, Albertson DG, Jablons DM, Gray JW. PMID: 12097266.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansCells
    63. Deriving quantitative conclusions from microarray expression data. Bioinformatics. 2002 Jul; 18(7):961-70. Olshen AB, Jain AN. PMID: 12117794.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    64. Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res. 2002 Feb 15; 62(4):957-60. Wilhelm M, Veltman JA, Olshen AB, Jain AN, Moore DH, Presti JC, Kovacs G, Waldman FM. PMID: 11861363.
      View in: PubMed   Mentions: 39     Fields:    Translation:Humans
    65. Fully automatic quantification of microarray image data. Genome Res. 2002 Feb; 12(2):325-32. Jain AN, Tokuyasu TA, Snijders AM, Segraves R, Albertson DG, Pinkel D. PMID: 11827952.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansCells
    66. Molecular hashkeys: a novel method for molecular characterization and its application for predicting important pharmaceutical properties of molecules. J Med Chem. 1999 May 20; 42(10):1739-48. Ghuloum AM, Sage CR, Jain AN. PMID: 10346926.
      View in: PubMed   Mentions: 12     Fields:    
    67. IcePick: a flexible surface-based system for molecular diversity. J Med Chem. 1999 Jan 14; 42(1):60-6. Mount J, Ruppert J, Welch W, Jain AN. PMID: 9888833.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    68. Automatic identification and representation of protein binding sites for molecular docking. Protein Sci. 1997 Mar; 6(3):524-33. Ruppert J, Welch W, Jain AN. PMID: 9070435.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    69. Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J Comput Aided Mol Des. 1996 Oct; 10(5):427-40. Jain AN. PMID: 8951652.
      View in: PubMed   Mentions: 129     Fields:    Translation:Cells
    70. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol. 1996 Jun; 3(6):449-62. Welch W, Ruppert J, Jain AN. PMID: 8807875.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    71. Quantitative binding site model generation: compass applied to multiple chemotypes targeting the 5-HT1A receptor. J Med Chem. 1995 Apr 14; 38(8):1295-308. Jain AN, Harris NL, Park JY. PMID: 7731016.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    72. A shape-based machine learning tool for drug design. J Comput Aided Mol Des. 1994 Dec; 8(6):635-52. Jain AN, Dietterich TG, Lathrop RH, Chapman D, Critchlow RE, Bauer BE, Webster TA, Lozano-Perez T. PMID: 7738601.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    73. Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark. J Med Chem. 1994 Jul 22; 37(15):2315-27. Jain AN, Koile K, Chapman D. PMID: 8057280.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
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