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    Matt Jacobson, PhD

    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
    Address1700 4th Street
    San Francisco CA 94158
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      Collapse Biography 
      Collapse Education and Training
      MITPh.D.Physical Chemistry1999
      OxfordPost-doctoralPhysical Chemistry2000
      Collapse Awards and Honors
      Stanford University1989David Starr Jordan Scholar
      Stanford University1993Phi Beta Kappa
      Stanford University1993American Institute of Chemists Graduation Award
      1995 - 1998National Defense Science and Engineering Graduate Fellow
      Ohio State University1997Rao Prize, for “outstanding student talk” at the International Symposium on Molecular Spectroscopy
      1998 - 1999Fannie and John Hertz Fellow
      1999 - 2000EPSRC (Engineering and Physical Sciences Research Council, U.K.) Visiting Fellow
      2000Air Force Research Laboratory, Space Vehicles Directorate “Team Publication of the Year Award”
      2000 - 2002National Science Foundation Postdoctoral Fellowship in Biological Informatics
      2004NSF CAREER Award
      2004Alfred P. Sloan Research Fellowship
      2006UCSF School of Pharmacy Dean’s Recognition for Excellence in Teaching

      Collapse Overview 
      Collapse Overview
      Dr. Jacobson’s research interests are in the area of computational structural biology and computer-aided drug design.

      Collapse ORNG Applications 
      Collapse Featured Publications
      Collapse Websites
      Collapse In The News
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      Collapse Bibliographic 
      Collapse 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.
      List All   |   Timeline
      1. 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, Liras S, Jacobson MP, Lokey RS. Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides. Org Lett. 2015 Jun 19; 17(12):2928-31.
        View in: PubMed
      2. 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. J Med Chem. 2015 Jun 11; 58(11):4581-9.
        View in: PubMed
      3. 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. Proc Natl Acad Sci U S A. 2015 May 5; 112(18):5661-6.
        View in: PubMed
      4. 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. J Org Chem. 2015 Apr 17; 80(8):3902-13.
        View in: PubMed
      5. 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. J Biomol Screen. 2015 Jul; 20(6):788-800.
        View in: PubMed
      6. 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. J Am Chem Soc. 2015 Feb 4; 137(4):1388-91.
        View in: PubMed
      7. Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC. Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry. 2015 Jan 27; 54(3):909-31.
        View in: PubMed
      8. 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. J Am Chem Soc. 2015 Jan 21; 137(2):715-21.
        View in: PubMed
      9. 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 Comput Biol. 2014 Oct; 10(10):e1003874.
        View in: PubMed PMC4191879
      10. Hasnain S, McClendon CL, Hsu MT, Jacobson MP, Bandyopadhyay P. A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion. PLoS One. 2014; 9(9):e106466.
        View in: PubMed PMC4152264
      11. 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. J Am Chem Soc. 2014 Sep 10; 136(36):12624-30.
        View in: PubMed PMC4160273
      12. 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.
        View in: PubMed PMC4128814
      13. 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.
        View in: PubMed PMC4117707
      14. 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, Gerlt JA, Jacobson MP. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014; 3.
        View in: PubMed PMC4113996
      15. 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.
        View in: PubMed PMC4081050
      16. 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.
        View in: PubMed PMC4068255
      17. Lexa KW, Dolghih E, Jacobson MP. A structure-based model for predicting serum albumin binding. PLoS One. 2014; 9(4):e93323.
        View in: PubMed PMC3972100
      18. Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio. 2014; 5(1):e00933-13.
        View in: PubMed PMC3950512
      19. Peng LX, Hsu MT, Bonomi M, Agard DA, Jacobson MP. The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery. PLoS Comput Biol. 2014 Feb; 10(2):e1003464.
        View in: PubMed PMC3916224
      20. 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. Bioorg Med Chem. 2014 Mar 15; 22(6):1960-72.
        View in: PubMed PMC3984052
      21. 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, Mulhern D, Stevens RD, Ilkayeva OR, Newgard CB, Jacobson MP, Hellerstein M, Goetzman ES, Gibson BW, Verdin E. SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. Cell Metab. 2013 Dec 3; 18(6):920-33.
        View in: PubMed PMC4105152
      22. 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.
        View in: PubMed PMC3837922
      23. Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature. 2013 Oct 31; 502(7473):698-702.
        View in: PubMed PMC3966649
      24. 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. Bioorg Med Chem. 2013 Dec 15; 21(24):7999-8012.
        View in: PubMed PMC3984054
      25. Choi CH, Webb BA, Chimenti MS, Jacobson MP, Barber DL. pH sensing by FAK-His58 regulates focal adhesion remodeling. J Cell Biol. 2013 Sep 16; 202(6):849-59.
        View in: PubMed PMC3776353
      26. 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. J Pharmacol Exp Ther. 2013 Nov; 347(2):325-38.
        View in: PubMed PMC3807058
      27. 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.
        View in: PubMed PMC3964877
      28. 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. 2013 Sep 3; 21(9):1571-80.
        View in: PubMed PMC3769517
      29. 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.
        View in: PubMed PMC3895326
      30. 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. 2013 May; 8(5):847-57.
        View in: PubMed PMC3984044
      31. 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. Proc Natl Acad Sci U S A. 2013 Mar 26; 110(13):E1196-202.
        View in: PubMed PMC3612614
      32. Schönichen A, Webb BA, Jacobson MP, Barber DL. Considering protonation as a posttranslational modification regulating protein structure and function. Annu Rev Biophys. 2013; 42:289-314.
        View in: PubMed PMC4041481
      33. 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. Pharm Res. 2013 Apr; 30(4):932-50.
        View in: PubMed PMC3640342
      34. Datta D, McClendon CL, Jacobson MP, Wells JA. Substrate and inhibitor-induced dimerization and cooperativity in caspase-1 but not caspase-3. J Biol Chem. 2013 Apr 5; 288(14):9971-81.
        View in: PubMed PMC3617296
      35. 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, McKerrow JM, Podust LM, Renslo AR. Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein J Org Chem. 2013; 9:15-25.
        View in: PubMed PMC3566858
      36. Lokey RS, Liras J, Liras S, Jacobson MP. Designing molecules to cross biological membranes. Curr Top Med Chem. 2013; 13(7):775.
        View in: PubMed
      37. Spreafico M, Jacobson MP. In silico prediction of brain exposure: drug free fraction, unbound brain to plasma concentration ratio and equilibrium half-life. Curr Top Med Chem. 2013; 13(7):813-20.
        View in: PubMed PMC4005893
      38. Dolghih E, Jacobson MP. Predicting efflux ratios and blood-brain barrier penetration from chemical structure: combining passive permeability with active efflux by P-glycoprotein. ACS Chem Neurosci. 2013 Feb 20; 4(2):361-7.
        View in: PubMed PMC3582291
      39. 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. 2013 Jan 8; 21(1):54-64.
        View in: PubMed
      40. 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, Lokey RS. Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance(). Medchemcomm. 2012 Oct; 3(10):1282-1289.
        View in: PubMed
      41. Kuroda D, Shirai H, Jacobson MP, Nakamura H. Computer-aided antibody design. Protein Eng Des Sel. 2012 Oct; 25(10):507-21.
        View in: PubMed PMC3449398
      42. Leung SS, Mijalkovic J, Borrelli K, Jacobson MP. Testing physical models of passive membrane permeation. J Chem Inf Model. 2012 Jun 25; 52(6):1621-36.
        View in: PubMed PMC3383340
      43. McClendon CL, Hua L, Barreiro A, Jacobson MP. Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion. J Chem Theory Comput. 2012 Jul 12; 8(6):2115-2126.
        View in: PubMed
      44. 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 Negl Trop Dis. 2012; 6(4):e1589.
        View in: PubMed PMC3317910
      45. 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). J Biol Chem. 2012 May 18; 287(21):17050-64.
        View in: PubMed PMC3366819
      46. Rafi SB, Hearn BR, Vedantham P, Jacobson MP, Renslo AR. Predicting and improving the membrane permeability of peptidic small molecules. J Med Chem. 2012 Apr 12; 55(7):3163-9.
        View in: PubMed PMC3325374
      47. 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.
        View in: PubMed PMC3306705
      48. Narayanan A, LeClaire LL, Barber DL, Jacobson MP. Phosphorylation of the Arp2 subunit relieves auto-inhibitory interactions for Arp2/3 complex activation. PLoS Comput Biol. 2011 Nov; 7(11):e1002226.
        View in: PubMed PMC3220268
      49. Gerlt JA, Babbitt PC, Jacobson MP, Almo SC. Divergent evolution in enolase superfamily: strategies for assigning functions. J Biol Chem. 2012 Jan 2; 287(1):29-34.
        View in: PubMed PMC3249080
      50. Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV. The Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62.
        View in: PubMed PMC3238057
      51. 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, Lokey RS. On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds. Nat Chem Biol. 2011 Nov; 7(11):810-7.
        View in: PubMed PMC3210067
      52. MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA. Assessment of protein structure refinement in CASP9. Proteins. 2011; 79 Suppl 10:74-90.
        View in: PubMed PMC3238793
      53. Webb BA, Chimenti M, Jacobson MP, Barber DL. Dysregulated pH: a perfect storm for cancer progression. Nat Rev Cancer. 2011 Sep; 11(9):671-7.
        View in: PubMed
      54. 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.
        View in: PubMed PMC3183355
      55. Dolghih E, Bryant C, Renslo AR, Jacobson MP. Predicting binding to p-glycoprotein by flexible receptor docking. PLoS Comput Biol. 2011 Jun; 7(6):e1002083.
        View in: PubMed PMC3121697
      56. Cossins BP, Jacobson MP, Guallar V. A new view of the bacterial cytosol environment. PLoS Comput Biol. 2011 Jun; 7(6):e1002066.
        View in: PubMed PMC3111478
      57. Nilmeier J, Hua L, Coutsias EA, Jacobson MP. Assessing protein loop flexibility by hierarchical Monte Carlo sampling. J Chem Theory Comput. 2011 May 10; 7(5):1564-1574.
        View in: PubMed
      58. 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. Proc Natl Acad Sci U S A. 2011 Apr 12; 108(15):6056-61.
        View in: PubMed PMC3076885
      59. Wong SE, Sellers BD, Jacobson MP. Effects of somatic mutations on CDR loop flexibility during affinity maturation. Proteins. 2011 Mar; 79(3):821-9.
        View in: PubMed
      60. 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 Comput Biol. 2010; 6(12):e1001015.
        View in: PubMed PMC2996313
      61. 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 Metab. 2010 Dec 1; 12(6):654-61.
        View in: PubMed PMC3310379
      62. Wong SE, Sellers BD, Jacobson MP. Effects of somatic mutations on CDR loop flexibility during affinity maturation. Proteins. 2010 Oct 19.
        View in: PubMed
      63. Sellers BD, Nilmeier JP, Jacobson MP. Antibodies as a model system for comparative model refinement. Proteins. 2010 Aug 15; 78(11):2490-505.
        View in: PubMed PMC2998178
      64. 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.
        View in: PubMed PMC2877507
      65. 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. Dev Cell. 2010 May 18; 18(5):841-8.
        View in: PubMed PMC2975025
      66. 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. Antimicrob Agents Chemother. 2010 Jun; 54(6):2480-8.
        View in: PubMed PMC2876414
      67. Huang N, Jacobson MP. Binding-site assessment by virtual fragment screening. PLoS One. 2010; 5(4):e10109.
        View in: PubMed PMC2852417
      68. 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 Negl Trop Dis. 2010; 4(4):e651.
        View in: PubMed PMC2850312
      69. 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.
        View in: PubMed PMC2787699
      70. 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.
        View in: PubMed PMC2744578
      71. McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP. Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. J Chem Theory Comput. 2009 Sep 8; 5(9):2486-2502.
        View in: PubMed
      72. Farady CJ, Sellers BD, Jacobson MP, Craik CS. Improving the species cross-reactivity of an antibody using computational design. Bioorg Med Chem Lett. 2009 Jul 15; 19(14):3744-7.
        View in: PubMed PMC2724971
      73. Narayanan A, Jacobson MP. Computational studies of protein regulation by post-translational phosphorylation. Curr Opin Struct Biol. 2009 Apr; 19(2):156-63.
        View in: PubMed
      74. Narayanan A, Sellers BD, Jacobson MP. Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains. J Mol Biol. 2009 May 22; 388(5):941-53.
        View in: PubMed
      75. 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 Chem Biol. 2009 Mar 20; 4(3):209-20.
        View in: PubMed PMC2677188
      76. 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, Raushel FM, Jacobson MP, Babbitt PC, Sali A. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009 Apr; 10(2):107-25.
        View in: PubMed PMC2693957
      77. 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, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9.
        View in: PubMed PMC2739730
      78. MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in CASP8. Proteins. 2009; 77 Suppl 9:66-80.
        View in: PubMed PMC2801025
      79. 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. J Cell Biol. 2008 Dec 1; 183(5):865-79.
        View in: PubMed PMC2592832
      80. 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.
        View in: PubMed PMC2714228
      81. Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 2008 Aug 15; 72(3):959-71.
        View in: PubMed PMC2764870
      82. Wong S, Jacobson MP. Conformational selection in silico: loop latching motions and ligand binding in enzymes. Proteins. 2008 Apr; 71(1):153-64.
        View in: PubMed
      83. Tan ES, Groban ES, Jacobson MP, Scanlan TS. Toward deciphering the code to aminergic G protein-coupled receptor drug design. Chem Biol. 2008 Apr; 15(4):343-53.
        View in: PubMed PMC2713717
      84. Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol. 2008 Mar 28; 377(3):914-34.
        View in: PubMed PMC2752715
      85. 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.
        View in: PubMed
      86. 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.
        View in: PubMed
      87. Huang N, Jacobson MP. Physics-based methods for studying protein-ligand interactions. Curr Opin Drug Discov Devel. 2007 May; 10(3):325-31.
        View in: PubMed
      88. 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. 2007 Mar 1; 66(4):824-37.
        View in: PubMed
      89. Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B. Prediction of side-chain conformations on protein surfaces. Proteins. 2007 Mar 1; 66(4):814-23.
        View in: PubMed PMC2743384
      90. Srivastava J, Barber DL, Jacobson MP. Intracellular pH sensors: design principles and functional significance. Physiology (Bethesda). 2007 Feb; 22:30-9.
        View in: PubMed
      91. Mandell DJ, Chorny I, Groban ES, Wong SE, Levine E, Rapp CS, Jacobson MP. Strengths of hydrogen bonds involving phosphorylated amino acid side chains. J Am Chem Soc. 2007 Jan 31; 129(4):820-7.
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      92. 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.
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      93. 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.
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      94. 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. J Mol Biol. 2006 Jun 30; 360(1):228-50.
        View in: PubMed
      95. Groban ES, Narayanan A, Jacobson MP. Conformational changes in protein loops and helices induced by post-translational phosphorylation. PLoS Comput Biol. 2006 Apr; 2(4):e32.
        View in: PubMed PMC1440919
      96. Rezai T, Yu B, Millhauser GL, Jacobson MP, Lokey RS. Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers. J Am Chem Soc. 2006 Mar 1; 128(8):2510-1.
        View in: PubMed
      97. Kenyon V, Chorny I, Carvajal WJ, Holman TR, Jacobson MP. Novel human lipoxygenase inhibitors discovered using virtual screening with homology models. J Med Chem. 2006 Feb 23; 49(4):1356-63.
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      98. Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem. 2006 Jan 26; 49(2):534-53.
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      99. 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. J Comput Chem. 2006 Jan 15; 27(1):72-89.
        View in: PubMed PMC2743414
      100. 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.
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      101. Chorny I, Dill KA, Jacobson MP. Surfaces affect ion pairing. J Phys Chem B. 2005 Dec 22; 109(50):24056-60.
        View in: PubMed
      102. 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.
        View in: PubMed
      103. Wong SE, Bernacki K, Jacobson M. Competition between intramolecular hydrogen bonds and solvation in phosphorylated peptides: simulations with explicit and implicit solvent. J Phys Chem B. 2005 Mar 24; 109(11):5249-58.
        View in: PubMed
      104. 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.
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      105. 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. 2004 Oct 19; 43(41):13063-71.
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      106. Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins. 2004 May 1; 55(2):351-67.
        View in: PubMed
      107. Li X, Jacobson MP, Friesner RA. High-resolution prediction of protein helix positions and orientations. Proteins. 2004 May 1; 55(2):368-82.
        View in: PubMed
      108. Guallar V, Jacobson M, McDermott A, Friesner RA. Computational modeling of the catalytic reaction in triosephosphate isomerase. J Mol Biol. 2004 Mar 12; 337(1):227-39.
        View in: PubMed
      109. Coutsias EA, Seok C, Jacobson MP, Dill KA. A kinematic view of loop closure. J Comput Chem. 2004 Mar; 25(4):510-28.
        View in: PubMed
      110. Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol. 2002 Jul 12; 320(3):597-608.
        View in: PubMed
      111. Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. J Struct Funct Genomics. 2002; 2(2):103-11.
        View in: PubMed
      112. Silva ML, Jacobson MP, Duan Z, and Field RW. Journal of Chemical Physics. Unexpected Simplicity in the S1 -> S0 Dispersed Fluorescence Spectrum of 13C2H2. 2002; 16:7939–7947.
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