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Chakrapani Kalyanaraman, PhD

Title(s)ASST RES ----- - FISCAL YEAR, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address1700 4th St
San Francisco CA 94158
Phone--
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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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    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. 15-Lipoxygenase-1 biosynthesis of 7S,14S-diHDHA implicates 15-Lipoxygenase-2 in biosynthesis of resolvin D5. J Lipid Res. 2020 May 13. Perry SC, Kalyanaraman C, Tourdot BE, Conrad WS, Akinkugbe O, Freedman JC, Holinstat M, Jacobson MP, Holman TR. PMID: 32404334.
      View in: PubMed   Mentions:    Fields:    
    2. Biosynthesis of the Maresin Intermediate, 13S,14S-Epoxy-DHA, by Human 15-Lipoxygenase and 12-Lipoxygenase and Its Regulation through Negative Allosteric Modulators. Biochemistry. 2020 May 19; 59(19):1832-1844. Freedman C, Tran A, Tourdot BE, Kalyanaraman C, Perry S, Holinstat M, Jacobson MP, Holman TR. PMID: 32324389.
      View in: PubMed   Mentions:    Fields:    
    3. Probing the Electrostatic and Steric Requirements for Substrate Binding in Human Platelet-Type 12-Lipoxygenase. Biochemistry. 2019 02 12; 58(6):848-857. Aleem AM, Tsai WC, Tena J, Alvarez G, Deschamps J, Kalyanaraman C, Jacobson MP, Holman T. PMID: 30565457.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. Inhibitor binding mode and allosteric regulation of Na+-glucose symporters. Nat Commun. 2018 12 07; 9(1):5245. Bisignano P, Ghezzi C, Jo H, Polizzi NF, Althoff T, Kalyanaraman C, Friemann R, Jacobson MP, Wright EM, Grabe M. PMID: 30532032.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    5. Exploration of Benzothiazole Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70). J Med Chem. 2018 Jul 26; 61(14):6163-6177. Shao H, Li X, Moses MA, Gilbert LA, Kalyanaraman C, Young ZT, Chernova M, Journey SN, Weissman JS, Hann B, Jacobson MP, Neckers L, Gestwicki JE. PMID: 29953808.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    6. High-throughput screen for inhibitors of protein-protein interactions in a reconstituted heat shock protein 70 (Hsp70) complex. J Biol Chem. 2018 03 16; 293(11):4014-4025. Taylor IR, Dunyak BM, Komiyama T, Shao H, Ran X, Assimon VA, Kalyanaraman C, Rauch JN, Jacobson MP, Zuiderweg ERP, Gestwicki JE. PMID: 29414793.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    7. GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors. Proc Natl Acad Sci U S A. 2016 09 20; 113(38):E5645-54. He XY, Li YJ, Kalyanaraman C, Qiu LL, Chen C, Xiao Q, Liu WX, Zhang W, Yang JJ, Chen G, Jacobson MP, Shi YS. PMID: 27601647.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    8. Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency. Bioorg Med Chem. 2016 11 01; 24(21):5380-5387. Armstrong M, van Hoorebeke C, Horn T, Deschamps J, Freedman JC, Kalyanaraman C, Jacobson MP, Holman T. PMID: 27647374.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    9. A potent and selective inhibitor targeting human and murine 12/15-LOX. Bioorg Med Chem. 2016 Mar 15; 24(6):1183-90. Armstrong MM, Freedman CJ, Jung JE, Zheng Y, Kalyanaraman C, Jacobson MP, Simeonov A, Maloney DJ, van Leyen K, Jadhav A, Holman TR. PMID: 26899595.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    10. 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. Long T, Neitz RJ, Beasley R, Kalyanaraman C, Suzuki BM, Jacobson MP, Dissous C, McKerrow JH, Drewry DH, Zuercher WJ, Singh R, Caffrey CR. PMID: 26751972.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    11. A high throughput screen identifies potent and selective inhibitors to human epithelial 15-lipoxygenase-2. PLoS One. 2014; 9(8):e104094. Jameson JB, Kantz A, Schultz L, Kalyanaraman C, Jacobson MP, Maloney DJ, Jadhav A, Simeonov A, Holman TR. PMID: 25111178.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    12. Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. Trends Biochem Sci. 2014 Aug; 39(8):363-71. Jacobson MP, Kalyanaraman C, Zhao S, Tian B. PMID: 24998033.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    13. Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58. Biochemistry. 2014 Jul 01; 53(25):4192-203. Groninger-Poe FP, Bouvier JT, Vetting MW, Kalyanaraman C, Kumar R, Almo SC, Jacobson MP, Gerlt JA. PMID: 24926996.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    14. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model. 2014 Jun 23; 54(6):1687-99. Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. PMID: 24802635.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    15. A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection. Antimicrob Agents Chemother. 2013 Dec; 57(12):6063-73. 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. PMID: 24060869.
      View in: PubMed   Mentions: 13     Fields:    Translation:Animals
    16. 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. Tian B, Wallrapp F, Kalyanaraman C, Zhao S, Eriksson LA, Jacobson MP. PMID: 23901785.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    17. Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature. 2013 Jun 06; 498(7452):123-6. 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. PMID: 23676670.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    18. 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. 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. PMID: 22392983.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    19. 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. Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP. PMID: 21780805.
      View in: PubMed   Mentions: 3     Fields:    
    20. Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway. Biochemistry. 2010 May 18; 49(19):4003-5. Kalyanaraman C, Jacobson MP. PMID: 20415432.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    21. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis . Biochemistry. 2009 Dec 08; 48(48):11546-58. 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. PMID: 19883118.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    22. Automated site preparation in physics-based rescoring of receptor ligand complexes. Proteins. 2009 Oct; 77(1):52-61. Rapp CS, Schonbrun C, Jacobson MP, Kalyanaraman C, Huang N. PMID: 19382204.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    23. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure. 2008 Nov 12; 16(11):1668-77. Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. PMID: 19000819.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    24. 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. Kalyanaraman C, Jacobson MP. PMID: 17989930.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    25. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol. 2007 Aug; 3(8):486-91. Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. PMID: 17603539.
      View in: PubMed   Mentions: 48     Fields:    Translation:Cells
    26. 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 01; 128(43):14073-80. Rezai T, Bock JE, Zhou MV, Kalyanaraman C, Lokey RS, Jacobson MP. PMID: 17061890.
      View in: PubMed   Mentions: 54     Fields:    Translation:Cells
    27. Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys. 2006 Nov 28; 8(44):5166-77. Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. PMID: 17203140.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    28. 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. Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. PMID: 16426060.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    29. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods. J Biomol Screen. 2005 Oct; 10(7):675-81. Bernacki K, Kalyanaraman C, Jacobson MP. PMID: 16170049.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    30. Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry. 2005 Feb 15; 44(6):2059-71. Kalyanaraman C, Bernacki K, Jacobson MP. PMID: 15697231.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
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