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Items: 1 to 50 of 68

1.

Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen.

Jain AN, Cleves AE, Gao Q, Wang X, Liu Y, Sherer EC, Reibarkh MY.

J Comput Aided Mol Des. 2019 Jun;33(6):531-558. doi: 10.1007/s10822-019-00203-1. Epub 2019 May 3.

2.

Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose.

Cleves AE, Jain AN.

J Comput Aided Mol Des. 2018 Jul;32(7):731-757. doi: 10.1007/s10822-018-0126-x. Epub 2018 Jun 22.

3.

ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs.

Cleves AE, Jain AN.

J Comput Aided Mol Des. 2017 May;31(5):419-439. doi: 10.1007/s10822-017-0015-8. Epub 2017 Mar 13.

4.

Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-coupled Affinity Purification/Mass Spectrometry Analysis Revealed a Novel Role of Neurofibromin in mTOR Signaling.

Li X, Gao M, Choi JM, Kim BJ, Zhou MT, Chen Z, Jain AN, Jung SY, Yuan J, Wang W, Wang Y, Chen J.

Mol Cell Proteomics. 2017 Apr;16(4):594-607. doi: 10.1074/mcp.M116.064543. Epub 2017 Feb 7.

5.

Extrapolative prediction using physically-based QSAR.

Cleves AE, Jain AN.

J Comput Aided Mol Des. 2016 Feb;30(2):127-52. doi: 10.1007/s10822-016-9896-1. Epub 2016 Feb 10.

6.

Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock.

Cleves AE, Jain AN.

J Comput Aided Mol Des. 2015 Jun;29(6):485-509. doi: 10.1007/s10822-015-9846-3. Epub 2015 May 5.

7.

Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes.

Cleves AE, Jain AN.

J Comput Aided Mol Des. 2015 Feb;29(2):101-12. doi: 10.1007/s10822-014-9815-2. Epub 2014 Nov 27.

8.

Prediction of off-target drug effects through data fusion.

Yera ER, Cleves AE, Jain AN.

Pac Symp Biocomput. 2014:160-71.

9.

A structure-guided approach for protein pocket modeling and affinity prediction.

Varela R, Cleves AE, Spitzer R, Jain AN.

J Comput Aided Mol Des. 2013 Nov;27(11):917-34. doi: 10.1007/s10822-013-9688-9. Epub 2013 Nov 9.

10.

Protein function annotation by local binding site surface similarity.

Spitzer R, Cleves AE, Varela R, Jain AN.

Proteins. 2014 Apr;82(4):679-94. doi: 10.1002/prot.24450. Epub 2013 Nov 22.

11.

Iterative refinement of a binding pocket model: active computational steering of lead optimization.

Varela R, Walters WP, Goldman BB, Jain AN.

J Med Chem. 2012 Oct 25;55(20):8926-42. doi: 10.1021/jm301210j. Epub 2012 Oct 9.

12.

Surflex-Dock: Docking benchmarks and real-world application.

Spitzer R, Jain AN.

J Comput Aided Mol Des. 2012 Jun;26(6):687-99. doi: 10.1007/s10822-011-9533-y. Epub 2012 May 9.

13.

Does your model weigh the same as a duck?

Jain AN, Cleves AE.

J Comput Aided Mol Des. 2012 Jan;26(1):57-67. doi: 10.1007/s10822-011-9530-1. Epub 2011 Dec 21.

14.

Chemical structural novelty: on-targets and off-targets.

Yera ER, Cleves AE, Jain AN.

J Med Chem. 2011 Oct 13;54(19):6771-85. doi: 10.1021/jm200666a. Epub 2011 Sep 14.

15.

Surface-based protein binding pocket similarity.

Spitzer R, Cleves AE, Jain AN.

Proteins. 2011 Sep;79(9):2746-63. doi: 10.1002/prot.23103. Epub 2011 Jul 18.

16.

QMOD: physically meaningful QSAR.

Jain AN.

J Comput Aided Mol Des. 2010 Oct;24(10):865-78. doi: 10.1007/s10822-010-9379-8. Epub 2010 Aug 19.

17.

Bioproduction of benzaldehyde in a solid-liquid two-phase partitioning bioreactor using Pichia pastoris.

Jain AN, Khan TR, Daugulis AJ.

Biotechnol Lett. 2010 Nov;32(11):1649-54. doi: 10.1007/s10529-010-0353-2. Epub 2010 Jul 18.

PMID:
20640874
18.

Molecular shape and medicinal chemistry: a perspective.

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.

J Med Chem. 2010 May 27;53(10):3862-86. doi: 10.1021/jm900818s.

19.

Physical binding pocket induction for affinity prediction.

Langham JJ, Cleves AE, Spitzer R, Kirshner D, Jain AN.

J Med Chem. 2009 Oct 8;52(19):6107-25. doi: 10.1021/jm901096y.

20.

Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation.

Jain AN.

J Comput Aided Mol Des. 2009 Jun;23(6):355-74. doi: 10.1007/s10822-009-9266-3. Epub 2009 Apr 2.

21.

Accurate and interpretable computational modeling of chemical mutagenicity.

Langham JJ, Jain AN.

J Chem Inf Model. 2008 Sep;48(9):1833-9. doi: 10.1021/ci800094a. Epub 2008 Sep 5.

22.

Recommendations for evaluation of computational methods.

Jain AN, Nicholls A.

J Comput Aided Mol Des. 2008 Mar-Apr;22(3-4):133-9. doi: 10.1007/s10822-008-9196-5. Epub 2008 Mar 13. Review.

23.

Customizing scoring functions for docking.

Pham TA, Jain AN.

J Comput Aided Mol Des. 2008 May;22(5):269-86. doi: 10.1007/s10822-008-9174-y. Epub 2008 Feb 14.

24.

Bias, reporting, and sharing: computational evaluations of docking methods.

Jain AN.

J Comput Aided Mol Des. 2008 Mar-Apr;22(3-4):201-12. Epub 2007 Dec 13.

PMID:
18075713
25.

Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery.

Cleves AE, Jain AN.

J Comput Aided Mol Des. 2008 Mar-Apr;22(3-4):147-59. Epub 2007 Dec 12.

PMID:
18074107
26.

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search.

Jain AN.

J Comput Aided Mol Des. 2007 May;21(5):281-306. Epub 2007 Mar 27.

PMID:
17387436
28.

Scoring functions for protein-ligand docking.

Jain AN.

Curr Protein Pept Sci. 2006 Oct;7(5):407-20. Review.

PMID:
17073693
29.

Parameter estimation for scoring protein-ligand interactions using negative training data.

Pham TA, Jain AN.

J Med Chem. 2006 Oct 5;49(20):5856-68.

PMID:
17004701
30.

Robust ligand-based modeling of the biological targets of known drugs.

Cleves AE, Jain AN.

J Med Chem. 2006 May 18;49(10):2921-38.

PMID:
16686535
31.

Breast tumor copy number aberration phenotypes and genomic instability.

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.

BMC Cancer. 2006 Apr 18;6:96.

32.

A deterministic motif finding algorithm with application to the human genome.

Hon LS, Jain AN.

Bioinformatics. 2006 May 1;22(9):1047-54. Epub 2006 Feb 2.

PMID:
16455748
33.

Pathway recognition and augmentation by computational analysis of microarray expression data.

Novak BA, Jain AN.

Bioinformatics. 2006 Jan 15;22(2):233-41. Epub 2005 Nov 8.

PMID:
16278238
34.

Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer.

Mehta KR, Nakao K, Zuraek MB, Ruan DT, Bergsland EK, Venook AP, Moore DH, Tokuyasu TA, Jain AN, Warren RS, Terdiman JP, Waldman FM.

Clin Cancer Res. 2005 Mar 1;11(5):1791-7.

35.

Mapping segmental and sequence variations among laboratory mice using BAC array CGH.

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.

Genome Res. 2005 Feb;15(2):302-11.

36.
37.

Virtual screening in lead discovery and optimization.

Jain AN.

Curr Opin Drug Discov Devel. 2004 Jul;7(4):396-403. Review.

PMID:
15338948
38.

Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors.

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.

Hum Mol Genet. 2004 Jul 1;13(13):1303-13. Epub 2004 May 11.

PMID:
15138198
39.

High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization.

Nakao K, Mehta KR, Fridlyand J, Moore DH, Jain AN, Lafuente A, Wiencke JW, Terdiman JP, Waldman FM.

Carcinogenesis. 2004 Aug;25(8):1345-57. Epub 2004 Mar 4.

PMID:
15001537
40.

Ligand-based structural hypotheses for virtual screening.

Jain AN.

J Med Chem. 2004 Feb 12;47(4):947-61.

PMID:
14761196
41.

Determinants of BRAF mutations in primary melanomas.

Maldonado JL, Fridlyand J, Patel H, Jain AN, Busam K, Kageshita T, Ono T, Albertson DG, Pinkel D, Bastian BC.

J Natl Cancer Inst. 2003 Dec 17;95(24):1878-90.

PMID:
14679157
42.
43.

Shaping of tumor and drug-resistant genomes by instability and selection.

Snijders AM, Fridlyand J, Mans DA, Segraves R, Jain AN, Pinkel D, Albertson DG.

Oncogene. 2003 Jul 10;22(28):4370-9.

PMID:
12853973
44.

Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma.

Snijders AM, Nowee ME, Fridlyand J, Piek JM, Dorsman JC, Jain AN, Pinkel D, van Diest PJ, Verheijen RH, Albertson DG.

Oncogene. 2003 Jul 3;22(27):4281-6.

PMID:
12833150
45.

Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors.

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.

Cancer Res. 2003 Jun 1;63(11):2872-80.

46.

High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.

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.

Am J Pathol. 2003 Mar;162(3):763-70.

47.
48.

An incidental pelvic spleen and splenule appearance on liver-spleen imaging.

Jain AN, Spieth ME, Kasner DL.

Clin Nucl Med. 2003 Jan;28(1):43-4. No abstract available.

PMID:
12493961
49.

Deriving quantitative conclusions from microarray expression data.

Olshen AB, Jain AN.

Bioinformatics. 2002 Jul;18(7):961-70.

PMID:
12117794
50.

Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway.

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.

Cancer Res. 2002 Jul 1;62(13):3636-40.

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