Matthew P. Jacobson - Publications

Affiliations: 
Pharmaceutical Chemistry University of California, San Francisco, San Francisco, CA 

130 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Tsai WC, Aleem AM, Whittington C, Cortopassi WA, Kalyanaraman C, Baroz A, Iavarone AT, Skrzypczak-Jankun E, Jacobson MP, Offenbacher AR, Holman T. Mutagenesis, Hydrogen-Deuterium Exchange, and Molecular Docking Investigations Establish the Dimeric Interface of Human Platelet-Type 12-Lipoxygenase. Biochemistry. PMID 33635645 DOI: 10.1021/acs.biochem.1c00053  0.76
2020 Kalita M, Villanueva-Meyer J, Ohkawa Y, Kalyanaraman C, Chen K, Mohamed E, Parker MFL, Jacobson MP, Phillips JJ, Evans MJ, Wilson DM. Synthesis and Screening of α-Xylosides in Human Glioblastoma Cells. Molecular Pharmaceutics. PMID 33315406 DOI: 10.1021/acs.molpharmaceut.0c00839  0.76
2020 Perry SC, Horn T, Tourdot BE, Yamaguchi A, Kalyanaraman C, Conrad WS, Akinkugbe O, Holinstat M, Jacobson MP, Holman TR. Role of Human 15-Lipoxygenase-2 in the Biosynthesis of the Lipoxin Intermediate, 5S,15S-diHpETE, Implicated with the Altered Positional Specificity of Human 15-Lipoxygenase-1. Biochemistry. PMID 33048542 DOI: 10.1021/acs.biochem.0c00622  0.76
2020 Perry SC, Kalyanaraman C, Tourdot BE, Conrad WS, Akinkugbe O, Freedman JC, Holinstat M, Jacobson MP, Holman TR. 15-Lipoxygenase-1 biosynthesis of 7S,14S-diHDHA implicates 15-Lipoxygenase-2 in biosynthesis of resolvin D5. Journal of Lipid Research. PMID 32404334 DOI: 10.1194/jlr.RA120000777  0.76
2020 Freedman CJ, Tran A, Tourdot BE, Kalyanaraman C, Perry S, Holinstat M, Jacobson MP, Holman TR. Biosynthesis of the Maresin Intermediate, 13S,14S-epoxy-DHA, by Human 15-Lipoxygenase and 12-Lipoxygenase and its Regulation through Negative Allosteric Modulators. Biochemistry. PMID 32324389 DOI: 10.1021/acs.biochem.0c00233  0.76
2018 Aleem A, Tsai WC, Tena J, Alvarez G, Deschamps J, Kalyanaraman C, Jacobson MP, Holman TR. Probing the Electrostatic and Steric Requirements for Substrate Binding in Human Platelet-type 12-Lipoxygenase. Biochemistry. PMID 30565457 DOI: 10.1021/Acs.Biochem.8B01167  0.76
2018 Bisignano P, Ghezzi C, Jo H, Polizzi NF, Althoff T, Kalyanaraman C, Friemann R, Jacobson MP, Wright EM, Grabe M. Inhibitor binding mode and allosteric regulation of Na-glucose symporters. Nature Communications. 9: 5245. PMID 30532032 DOI: 10.1038/S41467-018-07700-1  0.76
2018 Shao H, Li X, Moses MA, Gilbert LA, Kalyanaraman C, Young ZT, Chernova M, Journey SN, Weissman JS, Hann B, Jacobson MP, Neckers LM, Gestwicki JE. Exploration of Benzothiazole-Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70). Journal of Medicinal Chemistry. PMID 29953808 DOI: 10.1021/Acs.Jmedchem.8B00583  0.76
2018 Taylor IR, Dunyak BM, Komiyama T, Shao H, Ran X, Assimon VA, Kalyanaraman C, Rauch JN, Jacobson MP, Zuiderweg ERP, Gestwicki JE. High Throughput Screen for Inhibitors of Protein-Protein Interactions in a Reconstituted Heat Shock Protein 70 (Hsp70) Complex. The Journal of Biological Chemistry. PMID 29414793 DOI: 10.1074/Jbc.Ra117.001575  0.76
2016 Armstrong M, van Hoorebeke C, Horn T, Deschamps J, Freedman JC, Kalyanaraman C, Jacobson MP, Holman T. Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency. Bioorganic & Medicinal Chemistry. PMID 27647374 DOI: 10.1016/J.Bmc.2016.08.063  0.76
2016 He XY, Li YJ, Kalyanaraman C, Qiu LL, Chen C, Xiao Q, Liu WX, Zhang W, Yang JJ, Chen G, Jacobson MP, Shi YS. GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors. Proceedings of the National Academy of Sciences of the United States of America. PMID 27601647 DOI: 10.1073/pnas.1524358113  0.96
2016 de Jesus Cortez F, Suzawa M, Irvy S, Bruning JM, Sablin E, Jacobson MP, Fletterick RJ, Ingraham HA, England PM. Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2). Plos One. 11: e0159316. PMID 27467220 DOI: 10.1371/Journal.Pone.0159316  0.96
2016 Ball KA, Johnson JR, Lewinski MK, Guatelli J, Verschueren E, Krogan NJ, Jacobson MP. Non-degradative Ubiquitination of Protein Kinases. Plos Computational Biology. 12: e1004898. PMID 27253329 DOI: 10.1371/Journal.Pcbi.1004898  0.96
2016 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. Bioorganic & Medicinal Chemistry. PMID 26899595 DOI: 10.1016/j.bmc.2016.01.042  0.96
2016 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 Neglected Tropical Diseases. 10: e0004356. PMID 26751972 DOI: 10.1371/Journal.Pntd.0004356  0.96
2015 Ahlbach CL, Lexa KW, Bockus AT, Chen V, Crews P, Jacobson MP, Lokey RS. Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products. Future Medicinal Chemistry. 1-10. PMID 26067057 DOI: 10.4155/Fmc.15.78  0.96
2015 Schwochert J, Turner R, Thang M, Berkeley RF, Ponkey AR, Rodriguez KM, Leung SS, Khunte B, Goetz G, Limberakis C, Kalgutkar AS, Eng H, Shapiro MJ, Mathiowetz AM, Price DA, ... ... Jacobson MP, et al. Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides. Organic Letters. 17: 2928-31. PMID 26046483 DOI: 10.1021/Acs.Orglett.5B01162  0.96
2015 Bockus AT, Lexa KW, Pye CR, Kalgutkar AS, Gardner JW, Hund KC, Hewitt WM, Schwochert JA, Glassey E, Price DA, Mathiowetz AM, Liras S, Jacobson MP, Lokey RS. Probing the Physicochemical Boundaries of Cell Permeability and Oral Bioavailability in Lipophilic Macrocycles Inspired by Natural Products. Journal of Medicinal Chemistry. 58: 4581-9. PMID 25950816 DOI: 10.1021/Acs.Jmedchem.5B00128  0.96
2015 Chow JY, Tian BX, Ramamoorthy G, Hillerich BS, Seidel RD, Almo SC, Jacobson MP, Poulter CD. Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus. Proceedings of the National Academy of Sciences of the United States of America. 112: 5661-6. PMID 25901324 DOI: 10.1073/Pnas.1505127112  0.96
2015 Ramamoorthy G, Pugh ML, Tian BX, Phan RM, Perez LB, Jacobson MP, Poulter CD. Synthesis and enzymatic studies of bisubstrate analogues for farnesyl diphosphate synthase. The Journal of Organic Chemistry. 80: 3902-13. PMID 25734506 DOI: 10.1021/Acs.Joc.5B00202  0.96
2015 Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJ. A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. Journal of Biomolecular Screening. 20: 788-800. PMID 25690569 DOI: 10.1177/1087057115570550  0.96
2015 Zhang X, Kumar R, Vetting MW, Zhao S, Jacobson MP, Almo SC, Gerlt JA. A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily. Journal of the American Chemical Society. 137: 1388-91. PMID 25608448 DOI: 10.1021/Ja5103986  0.96
2015 Hewitt WM, Leung SS, Pye CR, Ponkey AR, Bednarek M, Jacobson MP, Lokey RS. Cell-permeable cyclic peptides from synthetic libraries inspired by natural products. Journal of the American Chemical Society. 137: 715-21. PMID 25517352 DOI: 10.1021/Ja508766B  0.96
2014 Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. Plos Computational Biology. 10: e1003874. PMID 25299649 DOI: 10.1371/journal.pcbi.1003874  0.96
2014 Krishnan S, Miller RM, Tian B, Mullins RD, Jacobson MP, Taunton J. Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis. Journal of the American Chemical Society. 136: 12624-30. PMID 25153195 DOI: 10.1021/Ja505194W  0.96
2014 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. 9: e104094. PMID 25111178 DOI: 10.1371/journal.pone.0104094  0.96
2014 Jacobson MP, Kalyanaraman C, Zhao S, Tian B. Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. Trends in Biochemical Sciences. 39: 363-71. PMID 24998033 DOI: 10.1016/J.Tibs.2014.05.006  0.96
2014 Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, ... ... Jacobson MP, et al. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 3. PMID 24980702 DOI: 10.7554/Elife.03275  0.96
2014 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. 53: 4192-203. PMID 24926996 DOI: 10.1021/Bi5005377  0.96
2014 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. Journal of Chemical Information and Modeling. 54: 1687-99. PMID 24802635 DOI: 10.1021/Ci5001554  0.96
2014 Lexa KW, Dolghih E, Jacobson MP. A structure-based model for predicting serum albumin binding. Plos One. 9: e93323. PMID 24691448 DOI: 10.1371/Journal.Pone.0093323  0.96
2014 Silber BM, Gever JR, Rao S, Li Z, Renslo AR, Widjaja K, Wong C, Giles K, Freyman Y, Elepano M, Irwin JJ, Jacobson MP, Prusiner SB. Novel compounds lowering the cellular isoform of the human prion protein in cultured human cells. Bioorganic & Medicinal Chemistry. 22: 1960-72. PMID 24530226 DOI: 10.1016/j.bmc.2014.01.001  0.96
2014 Hasnain S, Jacobson MP, Bandyopadhyay P. A comparative Brownian dynamics investigation between small linear and circular DNA: Scaling of diffusion coefficient with size and topology of DNA Chemical Physics Letters. 591: 253-258. DOI: 10.1016/J.Cplett.2013.11.029  0.96
2013 Rardin MJ, He W, Nishida Y, Newman JC, Carrico C, Danielson SR, Guo A, Gut P, Sahu AK, Li B, Uppala R, Fitch M, Riiff T, Zhu L, Zhou J, ... ... Jacobson MP, et al. SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. Cell Metabolism. 18: 920-33. PMID 24315375 DOI: 10.1016/J.Cmet.2013.11.013  0.96
2013 Silber BM, Gever JR, Li Z, Gallardo-Godoy A, Renslo AR, Widjaja K, Irwin JJ, Rao S, Jacobson MP, Ghaemmaghami S, Prusiner SB. Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells. Bioorganic & Medicinal Chemistry. 21: 7999-8012. PMID 24183589 DOI: 10.1016/J.Bmc.2013.09.022  0.96
2013 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. Antimicrobial Agents and Chemotherapy. 57: 6063-73. PMID 24060869 DOI: 10.1128/Aac.00734-13  0.96
2013 Choi CH, Webb BA, Chimenti MS, Jacobson MP, Barber DL. pH sensing by FAK-His58 regulates focal adhesion remodeling. The Journal of Cell Biology. 202: 849-59. PMID 24043700 DOI: 10.1083/jcb.201302131  0.96
2013 Lu D, Giles K, Li Z, Rao S, Dolghih E, Gever JR, Geva M, Elepano ML, Oehler A, Bryant C, Renslo AR, Jacobson MP, Dearmond SJ, Silber BM, Prusiner SB. Biaryl amides and hydrazones as therapeutics for prion disease in transgenic mice. The Journal of Pharmacology and Experimental Therapeutics. 347: 325-38. PMID 23965382 DOI: 10.1124/jpet.113.205799  0.96
2013 Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD. Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2. Structure (London, England : 1993). 21: 1571-80. PMID 23911090 DOI: 10.1016/J.Str.2013.06.021  0.96
2013 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. 52: 5511-3. PMID 23901785 DOI: 10.1021/Bi400546J  0.96
2013 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. 498: 123-6. PMID 23676670 DOI: 10.1038/nature12180  0.76
2013 Li Z, Silber BM, Rao S, Gever JR, Bryant C, Gallardo-Godoy A, Dolghih E, Widjaja K, Elepano M, Jacobson MP, Prusiner SB, Renslo AR. 2-Aminothiazoles with improved pharmacotherapeutic properties for treatment of prion disease. Chemmedchem. 8: 847-57. PMID 23509039 DOI: 10.1002/cmdc.201300007  0.96
2013 Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD. Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proceedings of the National Academy of Sciences of the United States of America. 110: E1196-202. PMID 23493556 DOI: 10.1073/Pnas.1300632110  0.96
2013 Schönichen A, Webb BA, Jacobson MP, Barber DL. Considering protonation as a posttranslational modification regulating protein structure and function. Annual Review of Biophysics. 42: 289-314. PMID 23451893 DOI: 10.1146/annurev-biophys-050511-102349  0.96
2013 Silber BM, Rao S, Fife KL, Gallardo-Godoy A, Renslo AR, Dalvie DK, Giles K, Freyman Y, Elepano M, Gever JR, Li Z, Jacobson MP, Huang Y, Benet LZ, Prusiner SB. Pharmacokinetics and metabolism of 2-aminothiazoles with antiprion activity in mice. Pharmaceutical Research. 30: 932-50. PMID 23417511 DOI: 10.1007/S11095-012-0912-4  0.96
2013 Choy JW, Bryant C, Calvet CM, Doyle PS, Gunatilleke SS, Leung SS, Ang KK, Chen S, Gut J, Oses-Prieto JA, Johnston JB, Arkin MR, Burlingame AL, Taunton J, Jacobson MP, et al. Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein Journal of Organic Chemistry. 9: 15-25. PMID 23400640 DOI: 10.3762/Bjoc.9.3  0.96
2013 Datta D, McClendon CL, Jacobson MP, Wells JA. Substrate and inhibitor-induced dimerization and cooperativity in caspase-1 but not caspase-3. The Journal of Biological Chemistry. 288: 9971-81. PMID 23386603 DOI: 10.1074/Jbc.M112.426460  0.96
2013 Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJ, Jacobson MP, Kortemme T. Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. Structure (London, England : 1993). 21: 54-64. PMID 23159126 DOI: 10.1016/J.Str.2012.10.007  0.96
2012 McClendon CL, Hua L, Barreiro A, Jacobson MP. Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion. Journal of Chemical Theory and Computation. 8: 2115-2126. PMID 23316121 DOI: 10.1021/Ct300008D  0.96
2012 Rand AC, Leung SS, Eng H, Rotter CJ, Sharma R, Kalgutkar AS, Zhang Y, Varma MV, Farley KA, Khunte B, Limberakis C, Price DA, Liras S, Mathiowetz AM, Jacobson MP, et al. Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance(). Medchemcomm. 3: 1282-1289. PMID 23133740 DOI: 10.1039/C2MD20203D  0.96
2012 Leung SS, Mijalkovic J, Borrelli K, Jacobson MP. Testing physical models of passive membrane permeation. Journal of Chemical Information and Modeling. 52: 1621-36. PMID 22621168 DOI: 10.1021/ci200583t  0.96
2012 Ingram JR, Rafi SB, Eroy-Reveles AA, Ray M, Lambeth L, Hsieh I, Ruelas D, Lim KC, Sakanari J, Craik CS, Jacobson MP, McKerrow JH. Investigation of the proteolytic functions of an expanded cercarial elastase gene family in Schistosoma mansoni. Plos Neglected Tropical Diseases. 6: e1589. PMID 22509414 DOI: 10.1371/Journal.Pntd.0001589  0.96
2012 Kumar P, Chimenti MS, Pemble H, Schönichen A, Thompson O, Jacobson MP, Wittmann T. Multisite phosphorylation disrupts arginine-glutamate salt bridge networks required for binding of cytoplasmic linker-associated protein 2 (CLASP2) to end-binding protein 1 (EB1). The Journal of Biological Chemistry. 287: 17050-64. PMID 22467876 DOI: 10.1074/jbc.M111.316661  0.96
2012 Rafi SB, Hearn BR, Vedantham P, Jacobson MP, Renslo AR. Predicting and improving the membrane permeability of peptidic small molecules. Journal of Medicinal Chemistry. 55: 3163-9. PMID 22394492 DOI: 10.1021/jm201634q  0.96
2012 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, ... ... Jacobson MP, et al. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proceedings of the National Academy of Sciences of the United States of America. 109: 4122-7. PMID 22392983 DOI: 10.1073/Pnas.1112081109  0.96
2012 Gerlt JA, Babbitt PC, Jacobson MP, Almo SC. Divergent evolution in enolase superfamily: strategies for assigning functions. The Journal of Biological Chemistry. 287: 29-34. PMID 22069326 DOI: 10.1074/Jbc.R111.240945  0.96
2011 Narayanan A, LeClaire LL, Barber DL, Jacobson MP. Phosphorylation of the Arp2 subunit relieves auto-inhibitory interactions for Arp2/3 complex activation. Plos Computational Biology. 7: e1002226. PMID 22125478 DOI: 10.1371/journal.pcbi.1002226  0.96
2011 MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA. Assessment of protein structure refinement in CASP9. Proteins. 79: 74-90. PMID 22069034 DOI: 10.1002/Prot.23131  0.96
2011 White TR, Renzelman CM, Rand AC, Rezai T, McEwen CM, Gelev VM, Turner RA, Linington RG, Leung SS, Kalgutkar AS, Bauman JN, Zhang Y, Liras S, Price DA, Mathiowetz AM, ... Jacobson MP, et al. On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds. Nature Chemical Biology. 7: 810-7. PMID 21946276 DOI: 10.1038/Nchembio.664  0.96
2011 Webb BA, Chimenti M, Jacobson MP, Barber DL. Dysregulated pH: a perfect storm for cancer progression. Nature Reviews. Cancer. 11: 671-7. PMID 21833026 DOI: 10.1038/nrc3110  0.96
2011 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. Journal of Chemical Information and Modeling. 51: 2082-9. PMID 21780805 DOI: 10.1021/ci200033n  0.76
2011 Nilmeier J, Hua L, Coutsias EA, Jacobson MP. Assessing protein loop flexibility by hierarchical Monte Carlo sampling. Journal of Chemical Theory and Computation. 7: 1564-1574. PMID 21743800 DOI: 10.1021/Ct1006696  0.96
2011 Dolghih E, Bryant C, Renslo AR, Jacobson MP. Predicting binding to p-glycoprotein by flexible receptor docking. Plos Computational Biology. 7: e1002083. PMID 21731480 DOI: 10.1371/journal.pcbi.1002083  0.96
2011 Cossins BP, Jacobson MP, Guallar V. A new view of the bacterial cytosol environment. Plos Computational Biology. 7: e1002066. PMID 21695225 DOI: 10.1371/Journal.Pcbi.1002066  0.96
2011 Sadowsky JD, Burlingame MA, Wolan DW, McClendon CL, Jacobson MP, Wells JA. Turning a protein kinase on or off from a single allosteric site via disulfide trapping. Proceedings of the National Academy of Sciences of the United States of America. 108: 6056-61. PMID 21430264 DOI: 10.1073/Pnas.1102376108  0.96
2011 Wong SE, Sellers BD, Jacobson MP. Effects of somatic mutations on CDR loop flexibility during affinity maturation. Proteins. 79: 821-9. PMID 21287614 DOI: 10.1002/prot.22920  0.8
2010 Morcos F, Chatterjee S, McClendon CL, Brenner PR, López-Rendón R, Zintsmaster J, Ercsey-Ravasz M, Sweet CR, Jacobson MP, Peng JW, Izaguirre JA. Modeling conformational ensembles of slow functional motions in Pin1-WW. Plos Computational Biology. 6: e1001015. PMID 21152000 DOI: 10.1371/Journal.Pcbi.1001015  0.96
2010 Shimazu T, Hirschey MD, Hua L, Dittenhafer-Reed KE, Schwer B, Lombard DB, Li Y, Bunkenborg J, Alt FW, Denu JM, Jacobson MP, Verdin E. SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production. Cell Metabolism. 12: 654-61. PMID 21109197 DOI: 10.1016/J.Cmet.2010.11.003  0.96
2010 Sellers BD, Nilmeier JP, Jacobson MP. Antibodies as a model system for comparative model refinement. Proteins. 78: 2490-505. PMID 20602354 DOI: 10.1002/prot.22757  0.8
2010 Wilbur JD, Hwang PK, Ybe JA, Lane M, Sellers BD, Jacobson MP, Fletterick RJ, Brodsky FM. Conformation switching of clathrin light chain regulates clathrin lattice assembly. Developmental Cell. 18: 841-8. PMID 20493816 DOI: 10.1016/J.Devcel.2010.04.007  0.96
2010 Kalyanaraman C, Jacobson MP. Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway. Biochemistry. 49: 4003-5. PMID 20415432 DOI: 10.1021/bi100445g  0.76
2010 Huang N, Jacobson MP. Binding-site assessment by virtual fragment screening. Plos One. 5: e10109. PMID 20404926 DOI: 10.1371/journal.pone.0010109  1
2010 Chen CK, Leung SS, Guilbert C, Jacobson MP, McKerrow JH, Podust LM. Structural characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei bound to the antifungal drugs posaconazole and fluconazole. Plos Neglected Tropical Diseases. 4: e651. PMID 20386598 DOI: 10.1371/Journal.Pntd.0000651  0.96
2010 Doyle PS, Chen CK, Johnston JB, Hopkins SD, Leung SS, Jacobson MP, Engel JC, McKerrow JH, Podust LM. A nonazole CYP51 inhibitor cures Chagas' disease in a mouse model of acute infection. Antimicrobial Agents and Chemotherapy. 54: 2480-8. PMID 20385875 DOI: 10.1128/Aac.00281-10  0.96
2009 McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP. Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. Journal of Chemical Theory and Computation. 5: 2486-2502. PMID 20161451 DOI: 10.1021/Ct9001812  0.96
2009 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. 48: 11546-58. PMID 19883118 DOI: 10.1021/Bi901731C  0.96
2009 MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in CASP8. Proteins. 77: 66-80. PMID 19714776 DOI: 10.1002/Prot.22538  0.96
2009 Farady CJ, Sellers BD, Jacobson MP, Craik CS. Improving the species cross-reactivity of an antibody using computational design. Bioorganic & Medicinal Chemistry Letters. 19: 3744-7. PMID 19477127 DOI: 10.1016/J.Bmcl.2009.05.005  0.96
2009 Rapp CS, Schonbrun C, Jacobson MP, Kalyanaraman C, Huang N. Automated site preparation in physics-based rescoring of receptor ligand complexes. Proteins. 77: 52-61. PMID 19382204 DOI: 10.1002/prot.22415  1
2009 Narayanan A, Jacobson MP. Computational studies of protein regulation by post-translational phosphorylation. Current Opinion in Structural Biology. 19: 156-63. PMID 19339172 DOI: 10.1016/j.sbi.2009.02.007  0.96
2009 Narayanan A, Sellers BD, Jacobson MP. Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains. Journal of Molecular Biology. 388: 941-53. PMID 19324053 DOI: 10.1016/j.jmb.2009.03.043  0.8
2009 Tan ES, Naylor JC, Groban ES, Bunzow JR, Jacobson MP, Grandy DK, Scanlan TS. The molecular basis of species-specific ligand activation of trace amine-associated receptor 1 (TAAR(1)). Acs Chemical Biology. 4: 209-20. PMID 19256523 DOI: 10.1021/Cb800304D  0.96
2009 Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, ... ... Jacobson MP, et al. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. Journal of Structural and Functional Genomics. 10: 107-25. PMID 19219566 DOI: 10.1007/S10969-008-9056-5  0.96
2009 Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, ... ... Jacobson MP, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/J.Str.2008.12.014  0.96
2008 Frantz C, Barreiro G, Dominguez L, Chen X, Eddy R, Condeelis J, Kelly MJ, Jacobson MP, Barber DL. Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding. The Journal of Cell Biology. 183: 865-79. PMID 19029335 DOI: 10.1083/Jcb.200804161  0.96
2008 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 (London, England : 1993). 16: 1668-77. PMID 19000819 DOI: 10.1016/J.Str.2008.08.015  0.96
2008 Srivastava J, Barreiro G, Groscurth S, Gingras AR, Goult BT, Critchley DR, Kelly MJ, Jacobson MP, Barber DL. Structural model and functional significance of pH-dependent talin-actin binding for focal adhesion remodeling. Proceedings of the National Academy of Sciences of the United States of America. 105: 14436-41. PMID 18780792 DOI: 10.1073/pnas.0805163105  0.96
2008 Tan ES, Groban ES, Jacobson MP, Scanlan TS. Toward deciphering the code to aminergic G protein-coupled receptor drug design. Chemistry & Biology. 15: 343-53. PMID 18420141 DOI: 10.1016/J.Chembiol.2008.03.004  0.96
2008 Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 72: 959-71. PMID 18300241 DOI: 10.1002/Prot.21990  0.96
2008 Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. Journal of Molecular Biology. 377: 914-34. PMID 18280498 DOI: 10.1016/J.Jmb.2008.01.049  0.96
2007 Kalyanaraman C, Jacobson MP. An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. Journal of Computer-Aided Molecular Design. 21: 675-9. PMID 17989930 DOI: 10.1007/s10822-007-9141-z  0.76
2007 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. Nature Chemical Biology. 3: 486-91. PMID 17603539 DOI: 10.1038/Nchembio.2007.11  0.96
2007 Huang N, Jacobson MP. Physics-based methods for studying protein-ligand interactions. Current Opinion in Drug Discovery & Development. 10: 325-31. PMID 17554859  1
2007 Srivastava J, Barber DL, Jacobson MP. Intracellular pH sensors: design principles and functional significance. Physiology (Bethesda, Md.). 22: 30-9. PMID 17289928 DOI: 10.1152/physiol.00035.2006  0.96
2007 Mandell DJ, Chorny I, Groban ES, Wong SE, Levine E, Rapp CS, Jacobson MP. Strengths of hydrogen bonds involving phosphorylated amino acid side chains. Journal of the American Chemical Society. 129: 820-7. PMID 17243818 DOI: 10.1021/Ja063019W  0.96
2007 Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B. Prediction of side-chain conformations on protein surfaces. Proteins. 66: 814-23. PMID 17206724 DOI: 10.1002/Prot.21099  0.96
2007 Li X, Jacobson MP, Zhu K, Zhao S, Friesner RA. Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling. Proteins. 66: 824-37. PMID 17154422 DOI: 10.1002/Prot.21125  0.96
2007 Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale optimization of a truncated newton minimization algorithm and application to proteins and protein-ligand complexes Journal of Chemical Theory and Computation. 3: 640-648. DOI: 10.1021/ct600129f  0.96
2006 Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. Molecular mechanics methods for predicting protein-ligand binding. Physical Chemistry Chemical Physics : Pccp. 8: 5166-77. PMID 17203140 DOI: 10.1039/b608269f  1
2006 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 Journal of the American Chemical Society. 128: 14073-14080. PMID 17061890 DOI: 10.1021/ja063076p  0.96
2006 Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. Evolution of Structure and Function in the o-Succinylbenzoate Synthase/N-Acylamino Acid Racemase Family of the Enolase Superfamily Journal of Molecular Biology. 360: 228-250. PMID 16740275 DOI: 10.1016/J.Jmb.2006.04.055  0.96
2006 Rezai T, Yu B, Millhauser GL, Jacobson MP, Lokey RS. Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers Journal of the American Chemical Society. 128: 2510-2511. PMID 16492015 DOI: 10.1021/Ja0563455  0.96
2006 Kenyon V, Chorny I, Carvajal WJ, Holman TR, Jacobson MP. Novel human lipoxygenase inhibitors discovered using virtual screening with homology models Journal of Medicinal Chemistry. 49: 1356-1363. PMID 16480270 DOI: 10.1021/Jm050639J  0.96
2006 Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. Journal of Chemical Information and Modeling. 46: 243-53. PMID 16426060 DOI: 10.1021/ci0502855  1
2006 Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. Journal of Medicinal Chemistry. 49: 534-53. PMID 16420040 DOI: 10.1021/Jm050540C  0.96
2006 Yu Z, Jacobson MP, Friesner RA. What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. Journal of Computational Chemistry. 27: 72-89. PMID 16261581 DOI: 10.1002/Jcc.20307  0.96
2005 Wong SE, Bernacki K, Jacobson M. Competition between intramolecular hydrogen bonds and solvation in phosphorylated peptides: simulations with explicit and implicit solvent. The Journal of Physical Chemistry. B. 109: 5249-58. PMID 16863191 DOI: 10.1021/jp046333q  0.8
2005 Chorny I, Dill KA, Jacobson MP. Surfaces affect ion pairing. The Journal of Physical Chemistry. B. 109: 24056-60. PMID 16375397 DOI: 10.1021/Jp055043M  0.96
2005 Bernacki K, Kalyanaraman C, Jacobson MP. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods. Journal of Biomolecular Screening. 10: 675-81. PMID 16170049 DOI: 10.1177/1087057105281220  0.76
2005 Kalyanaraman C, Bernacki K, Jacobson MP. Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry. 44: 2059-71. PMID 15697231 DOI: 10.1021/bi0481186  0.76
2004 Ruddat VC, Mogul R, Chorny I, Chen C, Perrin N, Whitman S, Kenyon V, Jacobson MP, Bernasconi CF, Holman TR. Tryptophan 500 and arginine 707 define product and substrate active site binding in soybean lipoxygenase-1 Biochemistry. 43: 13063-13071. PMID 15476400 DOI: 10.1021/Bi0489098  0.96
2004 Li X, Jacobson MP, Friesner RA. High-resolution prediction of protein helix positions and orientations. Proteins. 55: 368-82. PMID 15048828 DOI: 10.1002/Prot.20014  0.96
2004 Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins. 55: 351-67. PMID 15048827 DOI: 10.1002/Prot.10613  0.96
2004 Coutsias EA, Seok C, Jacobson MP, Dill KA. A kinematic view of loop closure. Journal of Computational Chemistry. 25: 510-28. PMID 14735570 DOI: 10.1002/Jcc.10416  0.96
2004 Yu Z, Jacobson MP, Josovitz J, Rapp CS, Friesner RA. First-shell solvation of ion pairs: Correction of systematic errors in implicit solvent models Journal of Physical Chemistry B. 108: 6643-6654. DOI: 10.1021/Jp037821L  0.96
2002 Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. Journal of Structural and Functional Genomics. 2: 103-11. PMID 12836667 DOI: 10.1023/A:1020435630054  0.96
2002 Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side-chain conformations. Journal of Molecular Biology. 320: 597-608. PMID 12096912 DOI: 10.1016/S0022-2836(02)00470-9  0.96
2002 Silva ML, Jacobson MP, Duan Z, Field RW. Unexpected simplicity in the S1-S0 dispersed fluorescence spectra of 13C2H2 Journal of Chemical Physics. 116: 7939-7947. DOI: 10.1063/1.1469018  0.96
2002 Jacobson MP, Kaminski GA, Friesner RA, Rapp CS. Force field validation using protein side chain prediction Journal of Physical Chemistry B. 106: 11673-11680. DOI: 10.1021/Jp021564N  0.96
2001 Hoshina K, Iwasaki A, Yamanouchi K, Jacobson MP, Field RW. The infrared-ultraviolet dispersed fluorescence spectrum of acetylene: New classes of bright states Journal of Chemical Physics. 114: 7424-7442. DOI: 10.1063/1.1333006  0.96
2001 Jacobson MP, Child MS. Spectroscopic signatures of bond-breaking internal rotation. II. Rotation-vibration level structure and quantum monodromy in HCP Journal of Chemical Physics. 114: 262-275. DOI: 10.1063/1.1330746  0.96
2001 Jacobson MP, Child MS. Spectroscopic signatures of bond-breaking internal rotation. I. Saddle point induced polyad breakdown Journal of Chemical Physics. 114: 250-261. DOI: 10.1063/1.1330238  0.96
2001 Child MS, Jacobson MP, Cooper CD. Scaling laws for strongly anharmonic vibrational matrix elements Journal of Physical Chemistry A. 105: 10791-10799. DOI: 10.1021/Jp012582S  0.96
2001 Jacobson MP, Child MS. Scaling rules for resonance dynamics near a saddle point: The pendulum as a zero-order model Journal of Physical Chemistry A. 105: 2834-2841. DOI: 10.1021/Jp0045080  0.96
2001 Jung C, Taylor HS, Jacobson MP. The acetylene bending spectrum at ∼10000 cm-1: Quantum assignments in the midst of classical chaos Journal of Physical Chemistry A. 105: 681-693. DOI: 10.1021/Jp002803E  0.96
2001 Ruckstuhl AF, Jacobson MP, Field RW, Dodd JA. Baseline subtraction using robust local regression estimation Journal of Quantitative Spectroscopy and Radiative Transfer. 68: 179-193. DOI: 10.1016/S0022-4073(00)00021-2  0.96
2001 Silva ML, Jacobson MP, Duan Z, Field RW. Anomalous simplicity of the à → X̃ dispersed fluorescence spectrum of 13c2h2 Journal of Molecular Structure. 565: 87-91. DOI: 10.1016/S0022-2860(00)00780-8  0.96
1999 Jamieson ER, Jacobson MP, Barnes CM, Chow CS, Lippard SJ. Structural and kinetic studies of a cisplatin-modified DNA icosamer binding to HMG1 domain B Journal of Biological Chemistry. 274: 12346-12354. PMID 10212205 DOI: 10.1074/Jbc.274.18.12346  0.96
1999 Jacobson MP, Jung C, Taylor HS, Field RW. State-by-state assignment of the bending spectrum of acetylene at 15000 cm-1: A case study of quantum-classical correspondence Journal of Chemical Physics. 111: 600-618. DOI: 10.1063/1.479341  0.96
1998 Jacobson MP, O'Brien JP, Silbey RJ, Field RW. Pure bending dynamics in the acetylene X̃1Σg + state up to 15000 cm-1 of internal energy Journal of Chemical Physics. 109: 121-133. DOI: 10.1063/1.476529  0.96
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