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Chakrapani Kalyanaraman, PhD

Address1700 4th St
San Francisco CA 94158
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    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

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    Collapse Selected 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.
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    1. Armstrong MM, Freedman CJ, Jung JE, Zheng Y, Kalyanaraman C, Jacobson MP, Simeonov A, Maloney DJ, van Leyen K, Jadhav A, Holman TR. A potent and selective inhibitor targeting human and murine 12/15-LOX. Bioorg Med Chem. 2016 Mar 15; 24(6):1183-90. PMID: 26899595.
      View in: PubMed
    2. Long T, Neitz RJ, Beasley R, Kalyanaraman C, Suzuki BM, Jacobson MP, Dissous C, McKerrow JH, Drewry DH, Zuercher WJ, Singh R, Caffrey CR. Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni. PLoS Negl Trop Dis. 2016 Jan; 10(1):e0004356. PMID: 26751972.
      View in: PubMed
    3. Jameson JB, Kantz A, Schultz L, Kalyanaraman C, Jacobson MP, Maloney DJ, Jadhav A, Simeonov A, Holman TR. A high throughput screen identifies potent and selective inhibitors to human epithelial 15-lipoxygenase-2. PLoS One. 2014; 9(8):e104094. PMID: 25111178; PMCID: PMC4128814.
    4. Jacobson MP, Kalyanaraman C, Zhao S, Tian B. Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. Trends Biochem Sci. 2014 Aug; 39(8):363-71. PMID: 24998033; PMCID: PMC4117707.
    5. Groninger-Poe FP, Bouvier JT, Vetting MW, Kalyanaraman C, Kumar R, Almo SC, Jacobson MP, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58. Biochemistry. 2014 Jul 1; 53(25):4192-203. PMID: 24926996; PMCID: PMC4081050.
    6. Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model. 2014 Jun 23; 54(6):1687-99. PMID: 24802635; PMCID: PMC4068255.
    7. Ndao M, Nath-Chowdhury M, Sajid M, Marcus V, Mashiyama ST, Sakanari J, Chow E, Mackey Z, Land KM, Jacobson MP, Kalyanaraman C, McKerrow JH, Arrowood MJ, Caffrey CR. A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection. Antimicrob Agents Chemother. 2013 Dec; 57(12):6063-73. PMID: 24060869; PMCID: PMC3837922.
    8. Tian B, Wallrapp F, Kalyanaraman C, Zhao S, Eriksson LA, Jacobson MP. Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase. Biochemistry. 2013 Aug 20; 52(33):5511-3. PMID: 23901785; PMCID: PMC3964877.
    9. Kim J, Xiao H, Bonanno JB, Kalyanaraman C, Brown S, Tang X, Al-Obaidi NF, Patskovsky Y, Babbitt PC, Jacobson MP, Lee YS, Almo SC. Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature. 2013 Jun 6; 498(7452):123-6. PMID: 23676670; PMCID: PMC3895326.
    10. Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci U S A. 2012 Mar 13; 109(11):4122-7. PMID: 22392983; PMCID: PMC3306705.
    11. Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP. A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series. J Chem Inf Model. 2011 Sep 26; 51(9):2082-9. PMID: 21780805; PMCID: PMC3183355.
    12. Kalyanaraman C, Jacobson MP. Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway. Biochemistry. 2010 May 18; 49(19):4003-5. PMID: 20415432; PMCID: PMC2877507.
    13. Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis . Biochemistry. 2009 Dec 8; 48(48):11546-58. PMID: 19883118; PMCID: PMC2787699.
    14. Rapp CS, Schonbrun C, Jacobson MP, Kalyanaraman C, Huang N. Automated site preparation in physics-based rescoring of receptor ligand complexes. Proteins. 2009 Oct; 77(1):52-61. PMID: 19382204; PMCID: PMC2744578.
    15. Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure. 2008 Nov 12; 16(11):1668-77. PMID: 19000819; PMCID: PMC2714228.
    16. Kalyanaraman C, Jacobson MP. An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. J Comput Aided Mol Des. 2007 Dec; 21(12):675-9. PMID: 17989930.
      View in: PubMed
    17. Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol. 2007 Aug; 3(8):486-91. PMID: 17603539.
      View in: PubMed
    18. Rezai T, Bock JE, Zhou MV, Kalyanaraman C, Lokey RS, Jacobson MP. Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides. J Am Chem Soc. 2006 Nov 1; 128(43):14073-80. PMID: 17061890.
      View in: PubMed
    19. Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys. 2006 Nov 28; 8(44):5166-77. PMID: 17203140.
      View in: PubMed
    20. Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. J Chem Inf Model. 2006 Jan-Feb; 46(1):243-53. PMID: 16426060.
      View in: PubMed
    21. Bernacki K, Kalyanaraman C, Jacobson MP. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods. J Biomol Screen. 2005 Oct; 10(7):675-81. PMID: 16170049.
      View in: PubMed
    22. Kalyanaraman C, Bernacki K, Jacobson MP. Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry. 2005 Feb 15; 44(6):2059-71. PMID: 15697231.
      View in: PubMed
    23. Antoniou D, Caratzoulas S, Kalyanaraman C, Mincer JS, Schwartz SD. Barrier passage and protein dynamics in enzymatically catalyzed reactions. Eur J Biochem. 2002 Jul; 269(13):3103-12. PMID: 12084050.
      View in: PubMed
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