Ann Jain, PhD

Title(s)Specialist, HDF Comprehensive Cancer Ctr
SchoolSchool of Medicine
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    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.
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    1. 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. J Comput Aided Mol Des. 2019 May 03. PMID: 31054028.
      View in: PubMed
    2. Cleves AE, Jain AN. Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose. J Comput Aided Mol Des. 2018 Jul; 32(7):731-757. PMID: 29934750.
      View in: PubMed
    3. Cleves AE, Jain AN. 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. PMID: 28289981.
      View in: PubMed
    4. Cleves AE, Jain AN. Extrapolative prediction using physically-based QSAR. J Comput Aided Mol Des. 2016 Feb; 30(2):127-52. PMID: 26860112; PMCID: PMC4796382.
    5. Cleves AE, Jain AN. 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. PMID: 25940276; PMCID: PMC4464052.
    6. Cleves AE, Jain AN. Chemical and protein structural basis for biological crosstalk between PPARa and COX enzymes. J Comput Aided Mol Des. 2015 Feb; 29(2):101-12. PMID: 25428568; PMCID: PMC4298667.
    7. Yera ER, Cleves AE, Jain AN. Prediction of off-target drug effects through data fusion. Pac Symp Biocomput. 2014; 160-71. PMID: 24297543; PMCID: PMC3897331.
    8. Spitzer R, Cleves AE, Varela R, Jain AN. Protein function annotation by local binding site surface similarity. Proteins. 2014 Apr; 82(4):679-94. PMID: 24166661; PMCID: PMC3949165.
    9. Varela R, Cleves AE, Spitzer R, Jain AN. A structure-guided approach for protein pocket modeling and affinity prediction. J Comput Aided Mol Des. 2013 Nov; 27(11):917-34. PMID: 24214361; PMCID: PMC3851759.
    10. Jain AN, Cleves AE. Does your model weigh the same as a duck? J Comput Aided Mol Des. 2012 Jan; 26(1):57-67. PMID: 22187141; PMCID: PMC3276372.
    11. Yera ER, Cleves AE, Jain AN. Chemical structural novelty: on-targets and off-targets. J Med Chem. 2011 Oct 13; 54(19):6771-85. PMID: 21916467; PMCID: PMC3188662.
    12. Spitzer R, Cleves AE, Jain AN. Surface-based protein binding pocket similarity. Proteins. 2011 Sep; 79(9):2746-63. PMID: 21769944; PMCID: PMC3155014.
    13. Langham JJ, Cleves AE, Spitzer R, Kirshner D, Jain AN. Physical binding pocket induction for affinity prediction. J Med Chem. 2009 Oct 08; 52(19):6107-25. PMID: 19754201; PMCID: PMC2766559.
    14. Cleves AE, Jain AN. 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. PMID: 18074107.
      View in: PubMed
    15. Cleves AE, Jain AN. Robust ligand-based modeling of the biological targets of known drugs. J Med Chem. 2006 May 18; 49(10):2921-38. PMID: 16686535.
      View in: PubMed
    16. Cleves AE, Clift-O'Grady L, Kelly RB. ATP-dependent formation of free synaptic vesicles from PC12 membranes in vitro. Neurochem Res. 1997 Aug; 22(8):933-40. PMID: 9239748.
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    17. Cleves AE. Protein transports: the nonclassical ins and outs. Curr Biol. 1997 May 01; 7(5):R318-20. PMID: 9115389.
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    18. Cleves AE, Cooper DN, Barondes SH, Kelly RB. A new pathway for protein export in Saccharomyces cerevisiae. J Cell Biol. 1996 Jun; 133(5):1017-26. PMID: 8655575; PMCID: PMC2120850.
    19. Cleves AE, Kelly RB. Rehearsing the ABCs. Protein translocation. Curr Biol. 1996 Mar 01; 6(3):276-8. PMID: 8805237.
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    20. Whitters EA, Cleves AE, McGee TP, Skinner HB, Bankaitis VA. SAC1p is an integral membrane protein that influences the cellular requirement for phospholipid transfer protein function and inositol in yeast. J Cell Biol. 1993 Jul; 122(1):79-94. PMID: 8314848; PMCID: PMC2119615.
    21. Kelly RB, Bonzelius F, Cleves A, Clift-O'Grady L, Grote E, Herman G. Biogenesis of synaptic vesicles. J Cell Sci Suppl. 1993; 17:81-3. PMID: 7511619.
      View in: PubMed
    22. Cleves AE, Bankaitis VA. Secretory pathway function in Saccharomyces cerevisiae. Adv Microb Physiol. 1992; 33:73-144. PMID: 1636512.
      View in: PubMed
    23. Cleves A, McGee T, Bankaitis V. Phospholipid transfer proteins: a biological debut. Trends Cell Biol. 1991 Jul; 1(1):30-4. PMID: 14731807.
      View in: PubMed
    24. Cleves AE, McGee TP, Whitters EA, Champion KM, Aitken JR, Dowhan W, Goebl M, Bankaitis VA. Mutations in the CDP-choline pathway for phospholipid biosynthesis bypass the requirement for an essential phospholipid transfer protein. Cell. 1991 Feb 22; 64(4):789-800. PMID: 1997207.
      View in: PubMed
    25. Bankaitis VA, Aitken JR, Cleves AE, Dowhan W. An essential role for a phospholipid transfer protein in yeast Golgi function. Nature. 1990 Oct 11; 347(6293):561-2. PMID: 2215682.
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    26. Salama SR, Cleves AE, Malehorn DE, Whitters EA, Bankaitis VA. Cloning and characterization of Kluyveromyces lactis SEC14, a gene whose product stimulates Golgi secretory function in Saccharomyces cerevisiae. J Bacteriol. 1990 Aug; 172(8):4510-21. PMID: 2198263; PMCID: PMC213282.
    27. Cleves AE, Novick PJ, Bankaitis VA. Mutations in the SAC1 gene suppress defects in yeast Golgi and yeast actin function. J Cell Biol. 1989 Dec; 109(6 Pt 1):2939-50. PMID: 2687291; PMCID: PMC2115899.