Matt Jacobson, PhD

InstitutionUniversity of California San Francisco
DepartmentPharmaceutical Chemistry
Address1700 4th St
San Francisco CA 94158
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    Collapse Biography 
    Collapse Education and Training
    MITPh.D.1999Physical Chemistry
    OxfordPost-doctoral2000Physical Chemistry
    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 Research 
    Collapse Research Activities and Funding
    Novel Strategies for the Discovery of Microbial Metabolic Pathways
    NIH P01GM118303Jun 15, 2016 - Apr 30, 2021
    Role: Co-Investigator
    NIH U54GM093342May 20, 2010 - Apr 30, 2016
    Role: Co-Investigator
    Understanding, Predicting, and Engineering Membrane Permeability
    NIH R01GM086602Feb 1, 2009 - Jan 31, 2014
    Role: Principal Investigator
    HARC Center: HIV Accessory and Regulatory Complexes
    NIH/NIGMS P50GM082250Aug 27, 2007 - Aug 31, 2022
    Role: Co-Investigator
    Physics-Based Refinement of Comparative Protein Models
    NIH R01GM081710Aug 1, 2007 - Jul 31, 2011
    Role: Principal Investigator
    Molecular Biophysics Training Grant
    NIH/NIGMS T32GM008284Sep 30, 1988 - Jun 30, 2023
    Role: Principal Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
    Collapse Websites
    Collapse In The News

    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. Tang S, Zhang N, Zhou Y, Cortopassi WA, Jacobson MP, Zhao LJ, Zhong RG. Structure-Based Discovery of Novel CK2a-Binding Cyclic Peptides with Anti-Cancer Activity. Mol Inform. 2018 Oct 11. PMID: 30307134.
      View in: PubMed
    2. 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). J Med Chem. 2018 Jun 28. PMID: 29953808.
      View in: PubMed
    3. Goode B, Mondal G, Hyun M, Ruiz DG, Lin YH, Van Ziffle J, Joseph NM, Onodera C, Talevich E, Grenert JP, Hewedi IH, Snuderl M, Brat DJ, Kleinschmidt-DeMasters BK, Rodriguez FJ, Louis DN, Yong WH, Lopes MB, Rosenblum MK, Butowski N, Tihan T, Bollen AW, Phillips JJ, Wiita AP, Yeh I, Jacobson MP, Bastian BC, Perry A, Solomon DA. A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle. Nat Commun. 2018 02 23; 9(1):810. PMID: 29476136.
      View in: PubMed
    4. 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. J Biol Chem. 2018 Feb 02. PMID: 29414793.
      View in: PubMed
    5. Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A. Prediction of enzymatic pathways by integrative pathway mapping. Elife. 2018 01 29; 7. PMID: 29377793.
      View in: PubMed
    6. de Jesus Cortez F, Nguyen P, Truillet C, Tian B, Kuchenbecker KM, Evans MJ, Webb P, Jacobson MP, Fletterick RJ, England PM. Development of 5N-Bicalutamide, a High-Affinity Reversible Covalent Antiandrogen. ACS Chem Biol. 2017 12 15; 12(12):2934-2939. PMID: 28981251.
      View in: PubMed
    7. Hindle SJ, Munji RN, Dolghih E, Gaskins G, Orng S, Ishimoto H, Soung A, DeSalvo M, Kitamoto T, Keiser MJ, Jacobson MP, Daneman R, Bainton RJ. Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior. Cell Rep. 2017 Oct 31; 21(5):1304-1316. PMID: 29091768.
      View in: PubMed
    8. Boehm M, Beaumont K, Jones R, Kalgutkar AS, Zhang L, Atkinson K, Bai G, Brown JA, Eng H, Goetz GH, Holder BR, Khunte B, Lazzaro S, Limberakis C, Ryu S, Shapiro MJ, Tylaska L, Yan J, Turner R, Leung SSF, Ramaseshan M, Price DA, Liras S, Jacobson MP, Earp DJ, Lokey RS, Mathiowetz AM, Menhaji-Klotz E. Discovery of Potent and Orally Bioavailable Macrocyclic Peptide-Peptoid Hybrid CXCR7 Modulators. J Med Chem. 2017 Dec 14; 60(23):9653-9663. PMID: 29045152.
      View in: PubMed
    9. White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal. 2017 Sep 05; 10(495). PMID: 28874603.
      View in: PubMed
    10. Szpiech ZA, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez RD. Prominent features of the amino acid mutation landscape in cancer. PLoS One. 2017; 12(8):e0183273. PMID: 28837668.
      View in: PubMed
    11. Tran HL, Lexa KW, Julien O, Young TS, Walsh CT, Jacobson MP, Wells JA. Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product. J Am Chem Soc. 2017 02 22; 139(7):2541-2544. PMID: 28170244.
      View in: PubMed
    12. Metcalf B, Chuang C, Dufu K, Patel MP, Silva-Garcia A, Johnson C, Lu Q, Partridge JR, Patskovska L, Patskovsky Y, Almo SC, Jacobson MP, Hua L, Xu Q, Gwaltney SL, Yee C, Harris J, Morgan BP, James J, Xu D, Hutchaleelaha A, Paulvannan K, Oksenberg D, Li Z. Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin. ACS Med Chem Lett. 2017 Mar 09; 8(3):321-326. PMID: 28337324.
      View in: PubMed
    13. Wang Q, Sciabola S, Barreiro G, Hou X, Bai G, Shapiro MJ, Koehn F, Villalobos A, Jacobson MP. Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction. J Chem Inf Model. 2016 11 28; 56(11):2194-2206. PMID: 27731994.
      View in: PubMed
    14. 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. Proc Natl Acad Sci U S A. 2016 09 20; 113(38):E5645-54. PMID: 27601647.
      View in: PubMed
    15. 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. Bioorg Med Chem. 2016 11 01; 24(21):5380-5387. PMID: 27647374.
      View in: PubMed
    16. Tian B, Poulter CD, Jacobson MP. Defining the Product Chemical Space of Monoterpenoid Synthases. PLoS Comput Biol. 2016 Aug; 12(8):e1005053. PMID: 27517297; PMCID: PMC4982680.
    17. Coutsias EA, Lexa KW, Wester MJ, Pollock SN, Jacobson MP. Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics. J Chem Theory Comput. 2016 Sep 13; 12(9):4674-87. PMID: 27447193.
      View in: PubMed
    18. 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. 2016; 11(7):e0159316. PMID: 27467220; PMCID: PMC4965143.
    19. Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S, Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crécy-Lagard V, Jacobson MP, Almo SC, Gerlt JA. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc Natl Acad Sci U S A. 2016 07 19; 113(29):E4161-9. PMID: 27402745; PMCID: PMC4961189 [Available on 01/19/17].
    20. Ball KA, Johnson JR, Lewinski MK, Guatelli J, Verschueren E, Krogan NJ, Jacobson MP. Non-degradative Ubiquitination of Protein Kinases. PLoS Comput Biol. 2016 06; 12(6):e1004898. PMID: 27253329; PMCID: PMC4890936.
    21. Leung SS, Sindhikara D, Jacobson MP. Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition. J Chem Inf Model. 2016 05 23; 56(5):924-9. PMID: 27135806.
      View in: PubMed
    22. 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; PMCID: PMC4778748 [Available on 03/15/17].
    23. 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; PMCID: PMC4709140.
    24. 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 Med Chem. 2015; 7(16):2121-30. PMID: 26067057.
      View in: PubMed
    25. 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. PMID: 26046483.
      View in: PubMed
    26. 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. PMID: 25950816.
      View in: PubMed
    27. 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 05; 112(18):5661-6. PMID: 25901324; PMCID: PMC4426440.
    28. 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. PMID: 25734506.
      View in: PubMed
    29. 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. PMID: 25690569.
      View in: PubMed
    30. 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 04; 137(4):1388-91. PMID: 25608448.
      View in: PubMed
    31. 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. PMID: 25540822; PMCID: PMC4310620.
    32. 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. PMID: 25517352.
      View in: PubMed
    33. 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. PMID: 25299649; PMCID: PMC4191879.
    34. 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. PMID: 25180859; PMCID: PMC4152264.
    35. 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. PMID: 25153195; PMCID: PMC4160273.
    36. 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.
    37. 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.
    38. 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 Jun 30; 3. PMID: 24980702; PMCID: PMC4113996.
    39. 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 01; 53(25):4192-203. PMID: 24926996; PMCID: PMC4081050.
    40. 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.
    41. Lexa KW, Dolghih E, Jacobson MP. A structure-based model for predicting serum albumin binding. PLoS One. 2014; 9(4):e93323. PMID: 24691448.
      View in: PubMed
    42. 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 Feb 11; 5(1):e00933-13. PMID: 24520058; PMCID: PMC3950512.
    43. 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. PMID: 24516374; PMCID: PMC3916224.
    44. 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. PMID: 24530226; PMCID: PMC3984052.
    45. 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 03; 18(6):920-33. PMID: 24315375; PMCID: PMC4105152.
    46. 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.
    47. 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. PMID: 24056934; PMCID: PMC3966649.
    48. 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. PMID: 24183589; PMCID: PMC3984054.
    49. 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. PMID: 24043700; PMCID: PMC3776353.
    50. 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. PMID: 23965382; PMCID: PMC3807058.
    51. 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.
    52. 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 03; 21(9):1571-80. PMID: 23911090; PMCID: PMC3769517.
    53. 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 06; 498(7452):123-6. PMID: 23676670; PMCID: PMC3895326.
    54. 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. PMID: 23509039; PMCID: PMC3984044.
    55. 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. PMID: 23493556; PMCID: PMC3612614.
    56. 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. PMID: 23451893; PMCID: PMC4041481.
    57. 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. PMID: 23417511; PMCID: PMC3640342.
    58. 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 05; 288(14):9971-81. PMID: 23386603; PMCID: PMC3617296.
    59. 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. PMID: 23400640; PMCID: PMC3566858.
    60. Lokey RS, Liras J, Liras S, Jacobson MP. Designing molecules to cross biological membranes. Curr Top Med Chem. 2013; 13(7):775. PMID: 23578022.
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    61. 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. PMID: 23578025; PMCID: PMC4005893.
    62. 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. PMID: 23421687; PMCID: PMC3582291.
    63. Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJS, Jacobson MP, Kortemme T. Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. Structure. 2013 Jan 08; 21(1):54-64. PMID: 23159126.
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    64. 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. PMID: 23133740.
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    65. Kuroda D, Shirai H, Jacobson MP, Nakamura H. Computer-aided antibody design. Protein Eng Des Sel. 2012 Oct; 25(10):507-21. PMID: 22661385; PMCID: PMC3449398.
    66. 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. PMID: 22621168; PMCID: PMC3383340.
    67. 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. PMID: 23316121.
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    68. 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. PMID: 22509414; PMCID: PMC3317910.
    69. 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. PMID: 22467876; PMCID: PMC3366819.
    70. 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. PMID: 22394492; PMCID: PMC3325374.
    71. 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.
    72. 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. PMID: 22125478; PMCID: PMC3220268.
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    75. 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 Sep 25; 7(11):810-7. PMID: 21946276; PMCID: PMC3210067.
    76. 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. PMID: 22069034; PMCID: PMC3238793.
    77. Webb BA, Chimenti M, Jacobson MP, Barber DL. Dysregulated pH: a perfect storm for cancer progression. Nat Rev Cancer. 2011 08 11; 11(9):671-7. PMID: 21833026.
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    80. Cossins BP, Jacobson MP, Guallar V. A new view of the bacterial cytosol environment. PLoS Comput Biol. 2011 Jun; 7(6):e1002066. PMID: 21695225; PMCID: PMC3111478.
    81. 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. PMID: 21743800.
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    82. 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. PMID: 21430264; PMCID: PMC3076885.
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    84. 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 Dec 02; 6(12):e1001015. PMID: 21152000; PMCID: PMC2996313.
    85. 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 01; 12(6):654-61. PMID: 21109197; PMCID: PMC3310379.
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    88. 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. PMID: 20493816; PMCID: PMC2975025.
    89. 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.
    90. 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. PMID: 20385875; PMCID: PMC2876414.
    91. Huang N, Jacobson MP. Binding-site assessment by virtual fragment screening. PLoS One. 2010 Apr 09; 5(4):e10109. PMID: 20404926.
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    92. 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 Apr 06; 4(4):e651. PMID: 20386598; PMCID: PMC2850312.
    93. 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 08; 48(48):11546-58. PMID: 19883118; PMCID: PMC2787699.
    94. 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.
    95. McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP. Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. J Chem Theory Comput. 2009 Sep 08; 5(9):2486-2502. PMID: 20161451.
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    96. Nilmeier J, Jacobson MP. Monte Carlo Sampling with Hierarchical Move Sets: POSH Monte Carlo. J Chem Theory Comput. 2009 Aug 11; 5(8):1968-84. PMID: 26613140.
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    98. Narayanan A, Jacobson MP. Computational studies of protein regulation by post-translational phosphorylation. Curr Opin Struct Biol. 2009 Apr; 19(2):156-63. PMID: 19339172.
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    103. 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. PMID: 19714776; PMCID: PMC2801025.
    104. 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 01; 183(5):865-79. PMID: 19029335; PMCID: PMC2592832.
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    107. Nilmeier J, Jacobson M. Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility. J Chem Theory Comput. 2008 May; 4(5):835-846. PMID: 19119325.
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    110. 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. PMID: 18280498; PMCID: PMC2752715.
    111. 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.
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    115. Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes. J Chem Theory Comput. 2007 Mar; 3(2):640-8. PMID: 26637042.
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    116. Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B. Prediction of side-chain conformations on protein surfaces. Proteins. 2007 Mar 01; 66(4):814-23. PMID: 17206724; PMCID: PMC2743384.
    117. Srivastava J, Barber DL, Jacobson MP. Intracellular pH sensors: design principles and functional significance. Physiology (Bethesda). 2007 Feb; 22:30-9. PMID: 17289928.
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    118. 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. PMID: 17243818.
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    119. 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 01; 128(43):14073-80. PMID: 17061890.
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    121. 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. PMID: 16740275.
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    122. 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. PMID: 16628247; PMCID: PMC1440919.
    123. 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 01; 128(8):2510-1. PMID: 16492015.
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    124. 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. PMID: 16480270.
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    125. 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. PMID: 16420040.
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    126. 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. PMID: 16261581; PMCID: PMC2743414.
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    128. Chorny I, Dill KA, Jacobson MP. Surfaces affect ion pairing. J Phys Chem B. 2005 Dec 22; 109(50):24056-60. PMID: 16375397.
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    129. 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.
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    130. 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. PMID: 16863191.
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    131. 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.
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    132. 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. PMID: 15476400.
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    133. 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 01; 55(2):351-67. PMID: 15048827.
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    134. Li X, Jacobson MP, Friesner RA. High-resolution prediction of protein helix positions and orientations. Proteins. 2004 May 01; 55(2):368-82. PMID: 15048828.
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    135. 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. PMID: 15001364.
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    136. Coutsias EA, Seok C, Jacobson MP, Dill KA. A kinematic view of loop closure. J Comput Chem. 2004 Mar; 25(4):510-28. PMID: 14735570.
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    137. 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. PMID: 12096912.
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    138. 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.
    139. 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. PMID: 12836667.
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