Matt Jacobson, PhD

Title(s)Professor, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address1700 4th St
San Francisco CA 94158
Phone--
ORCID ORCID Icon0000-0001-6262-655X Additional info
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    Collapse Biography 
    Collapse Education and Training
    StanfordB.S.1993Chemistry
    MITPh.D.1999Physical Chemistry
    OxfordPost-doctoral2000Physical Chemistry
    ColumbiaPost-doctoral2002Chemistry
    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
    COLLABORATIVE CENTER FOR AN ENZYME FUNCTION INITIATIVE
    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 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 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 Academic Senate

    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. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Analogs of the Dopamine Metabolite 5,6-Dihydroxyindole Bind Directly to and Activate the Nuclear Receptor Nurr1. ACS Chem Biol. 2021 Jul 16; 16(7):1159-1163. Kholodar SA, Lang G, Cortopassi WA, Iizuka Y, Brah HS, Jacobson MP, England PM. PMID: 34165961.
      View in: PubMed   Mentions:    Fields:    
    2. In Vitro Biosynthetic Pathway Investigations of Neuroprotectin D1 (NPD1) and Protectin DX (PDX) by Human 12-Lipoxygenase, 15-Lipoxygenase-1, and 15-Lipoxygenase-2. Biochemistry. 2021 May 24. Tsai WC, Kalyanaraman C, Yamaguchi A, Holinstat M, Jacobson MP, Holman TR. PMID: 34029049.
      View in: PubMed   Mentions:    Fields:    
    3. Protomer alignment modulates specificity of RNA substrate recognition by Ire1. Elife. 2021 Apr 27; 10. Li W, Crotty K, Garrido Ruiz D, Voorhies M, Rivera C, Sil A, Mullins RD, Jacobson MP, Peschek J, Walter P. PMID: 33904404.
      View in: PubMed   Mentions:    Fields:    
    4. A Crowding Barrier to Protein Inhibition in Colloidal Aggregates. J Med Chem. 2021 04 08; 64(7):4109-4116. Lak P, O'Donnell H, Du X, Jacobson MP, Shoichet BK. PMID: 33761256.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    5. Mutagenesis, Hydrogen-Deuterium Exchange, and Molecular Docking Investigations Establish the Dimeric Interface of Human Platelet-Type 12-Lipoxygenase. Biochemistry. 2021 03 16; 60(10):802-812. Tsai WC, Aleem AM, Whittington C, Cortopassi WA, Kalyanaraman C, Baroz A, Iavarone AT, Skrzypczak-Jankun E, Jacobson MP, Offenbacher AR, Holman T. PMID: 33635645.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. Synthesis and Screening of a-Xylosides in Human Glioblastoma Cells. Mol Pharm. 2021 01 04; 18(1):451-460. Kalita M, Villanueva-Meyer J, Ohkawa Y, Kalyanaraman C, Chen K, Mohamed E, Parker MFL, Jacobson MP, Phillips JJ, Evans MJ, Wilson DM. PMID: 33315406.
      View in: PubMed   Mentions:    Fields:    
    7. 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. 2020 10 27; 59(42):4118-4130. Perry SC, Horn T, Tourdot BE, Yamaguchi A, Kalyanaraman C, Conrad WS, Akinkugbe O, Holinstat M, Jacobson MP, Holman TR. PMID: 33048542.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    8. Synthetic group A streptogramin antibiotics that overcome Vat resistance. Nature. 2020 10; 586(7827):145-150. Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Mühle E, Chesneau O, Fraser JS, Seiple IB. PMID: 32968273.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    9. The Synthesis and Structural Requirements for Measuring Glucocorticoid Receptor Expression In Vivo with (±)-11C-YJH08 PET. J Nucl Med. 2021 May 10; 62(5):723-731. Huang Y, Zhao N, Wang YH, Truillet C, Wei J, Parker MFL, Blecha JE, Drake CR, VanBrocklin HF, Garrido-Ruiz D, Jacobson MP, Aggarwal R, Behr SC, Flavell RR, Wilson DM, Seo Y, Evans MJ. PMID: 32887758.
      View in: PubMed   Mentions:    Fields:    
    10. 15-Lipoxygenase-1 biosynthesis of 7S,14S-diHDHA implicates 15-lipoxygenase-2 in biosynthesis of resolvin D5. J Lipid Res. 2020 07; 61(7):1087-1103. Perry SC, Kalyanaraman C, Tourdot BE, Conrad WS, Akinkugbe O, Freedman JC, Holinstat M, Jacobson MP, Holman TR. PMID: 32404334.
      View in: PubMed   Mentions: 4     Fields:    
    11. Biosynthesis of the Maresin Intermediate, 13S,14S-Epoxy-DHA, by Human 15-Lipoxygenase and 12-Lipoxygenase and Its Regulation through Negative Allosteric Modulators. Biochemistry. 2020 05 19; 59(19):1832-1844. Freedman C, Tran A, Tourdot BE, Kalyanaraman C, Perry S, Holinstat M, Jacobson MP, Holman TR. PMID: 32324389.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    12. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. PMID: 32353859.
      View in: PubMed   Mentions: 859     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    13. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 22. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. PMID: 32511329.
      View in: PubMed   Mentions:
    14. Age- and stress-associated C. elegans granulins impair lysosomal function and induce a compensatory HLH-30/TFEB transcriptional response. PLoS Genet. 2019 08; 15(8):e1008295. Butler VJ, Gao F, Corrales CI, Cortopassi WA, Caballero B, Vohra M, Ashrafi K, Cuervo AM, Jacobson MP, Coppola G, Kao AW. PMID: 31398187.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    15. Multi-Granulin Domain Peptides Bind to Pro-Cathepsin D and Stimulate Its Enzymatic Activity More Effectively Than Progranulin in Vitro. Biochemistry. 2019 06 11; 58(23):2670-2674. Butler VJ, Cortopassi WA, Gururaj S, Wang AL, Pierce OM, Jacobson MP, Kao AW. PMID: 31099551.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    16. Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. Mol Cell. 2019 06 20; 74(6):1164-1174.e4. Ali I, Ruiz DG, Ni Z, Johnson JR, Zhang H, Li PC, Khalid MM, Conrad RJ, Guo X, Min J, Greenblatt J, Jacobson M, Krogan NJ, Ott M. PMID: 31054975.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    17. Tau repeat regions contain conserved histidine residues that modulate microtubule-binding in response to changes in pH. J Biol Chem. 2019 05 31; 294(22):8779-8790. Charafeddine RA, Cortopassi WA, Lak P, Tan R, McKenney RJ, Jacobson MP, Barber DL, Wittmann T. PMID: 30992364.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    18. Conformational Dynamics of the HIV-Vif Protein Complex. Biophys J. 2019 04 23; 116(8):1432-1445. Ball KA, Chan LM, Stanley DJ, Tierney E, Thapa S, Ta HM, Burton L, Binning JM, Jacobson MP, Gross JD. PMID: 30961890.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    19. Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite. Cell Chem Biol. 2019 05 16; 26(5):674-685.e6. Bruning JM, Wang Y, Oltrabella F, Tian B, Kholodar SA, Liu H, Bhattacharya P, Guo S, Holton JM, Fletterick RJ, Jacobson MP, England PM. PMID: 30853418.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    20. Progranulin Stimulates the In Vitro Maturation of Pro-Cathepsin D at Acidic pH. J Mol Biol. 2019 03 01; 431(5):1038-1047. Butler VJ, Cortopassi WA, Argouarch AR, Ivry SL, Craik CS, Jacobson MP, Kao AW. PMID: 30690031.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    21. Probing the Electrostatic and Steric Requirements for Substrate Binding in Human Platelet-Type 12-Lipoxygenase. Biochemistry. 2019 02 12; 58(6):848-857. Aleem AM, Tsai WC, Tena J, Alvarez G, Deschamps J, Kalyanaraman C, Jacobson MP, Holman T. PMID: 30565457.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    22. Inhibitor binding mode and allosteric regulation of Na+-glucose symporters. Nat Commun. 2018 12 07; 9(1):5245. Bisignano P, Ghezzi C, Jo H, Polizzi NF, Althoff T, Kalyanaraman C, Friemann R, Jacobson MP, Wright EM, Grabe M. PMID: 30532032.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    23. Structure-based Discovery of Novel CK2a-Binding Cyclic Peptides with Anti-cancer Activity. Mol Inform. 2019 03; 38(3):e1800089. Tang S, Zhang N, Zhou Y, Cortopassi WA, Jacobson MP, Zhao LJ, Zhong RG. PMID: 30307134.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    24. Exploration of Benzothiazole Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70). J Med Chem. 2018 Jul 26; 61(14):6163-6177. Shao H, Li X, Moses MA, Gilbert LA, Kalyanaraman C, Young ZT, Chernova M, Journey SN, Weissman JS, Hann B, Jacobson MP, Neckers L, Gestwicki JE. PMID: 29953808.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    25. A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle. Nat Commun. 2018 02 23; 9(1):810. 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. PMID: 29476136.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    26. High-throughput screen for inhibitors of protein-protein interactions in a reconstituted heat shock protein 70 (Hsp70) complex. J Biol Chem. 2018 03 16; 293(11):4014-4025. Taylor IR, Dunyak BM, Komiyama T, Shao H, Ran X, Assimon VA, Kalyanaraman C, Rauch JN, Jacobson MP, Zuiderweg ERP, Gestwicki JE. PMID: 29414793.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    27. Prediction of enzymatic pathways by integrative pathway mapping. Elife. 2018 01 29; 7. 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. PMID: 29377793.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    28. Development of 5N-Bicalutamide, a High-Affinity Reversible Covalent Antiandrogen. ACS Chem Biol. 2017 12 15; 12(12):2934-2939. de Jesus Cortez F, Nguyen P, Truillet C, Tian B, Kuchenbecker KM, Evans MJ, Webb P, Jacobson MP, Fletterick RJ, England PM. PMID: 28981251.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    29. Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior. Cell Rep. 2017 Oct 31; 21(5):1304-1316. 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. PMID: 29091768.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    30. Discovery of Potent and Orally Bioavailable Macrocyclic Peptide-Peptoid Hybrid CXCR7 Modulators. J Med Chem. 2017 12 14; 60(23):9653-9663. 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. PMID: 29045152.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    31. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal. 2017 Sep 05; 10(495). White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. PMID: 28874603.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    32. Prominent features of the amino acid mutation landscape in cancer. PLoS One. 2017; 12(8):e0183273. Szpiech ZA, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez RD. PMID: 28837668.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    33. 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. Tran HL, Lexa KW, Julien O, Young TS, Walsh CT, Jacobson MP, Wells JA. PMID: 28170244.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    34. Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin. ACS Med Chem Lett. 2017 Mar 09; 8(3):321-326. 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. PMID: 28337324.
      View in: PubMed   Mentions:
    35. Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction. J Chem Inf Model. 2016 11 28; 56(11):2194-2206. Wang Q, Sciabola S, Barreiro G, Hou X, Bai G, Shapiro MJ, Koehn F, Villalobos A, Jacobson MP. PMID: 27731994.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    36. GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors. Proc Natl Acad Sci U S A. 2016 09 20; 113(38):E5645-54. He XY, Li YJ, Kalyanaraman C, Qiu LL, Chen C, Xiao Q, Liu WX, Zhang W, Yang JJ, Chen G, Jacobson MP, Shi YS. PMID: 27601647.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    37. Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency. Bioorg Med Chem. 2016 11 01; 24(21):5380-5387. Armstrong M, van Hoorebeke C, Horn T, Deschamps J, Freedman JC, Kalyanaraman C, Jacobson MP, Holman T. PMID: 27647374.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    38. Defining the Product Chemical Space of Monoterpenoid Synthases. PLoS Comput Biol. 2016 08; 12(8):e1005053. Tian B, Poulter CD, Jacobson MP. PMID: 27517297.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    39. Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics. J Chem Theory Comput. 2016 Sep 13; 12(9):4674-87. Coutsias EA, Lexa KW, Wester MJ, Pollock SN, Jacobson MP. PMID: 27447193.
      View in: PubMed   Mentions: 13     Fields:    
    40. Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2). PLoS One. 2016; 11(7):e0159316. de Jesus Cortez F, Suzawa M, Irvy S, Bruning JM, Sablin E, Jacobson MP, Fletterick RJ, Ingraham HA, England PM. PMID: 27467220.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    41. 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. 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. PMID: 27402745.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    42. Non-degradative Ubiquitination of Protein Kinases. PLoS Comput Biol. 2016 06; 12(6):e1004898. Ball KA, Johnson JR, Lewinski MK, Guatelli J, Verschueren E, Krogan NJ, Jacobson MP. PMID: 27253329.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    43. Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition. J Chem Inf Model. 2016 05 23; 56(5):924-9. Leung SS, Sindhikara D, Jacobson MP. PMID: 27135806.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    44. A potent and selective inhibitor targeting human and murine 12/15-LOX. Bioorg Med Chem. 2016 Mar 15; 24(6):1183-90. Armstrong MM, Freedman CJ, Jung JE, Zheng Y, Kalyanaraman C, Jacobson MP, Simeonov A, Maloney DJ, van Leyen K, Jadhav A, Holman TR. PMID: 26899595.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    45. Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni. PLoS Negl Trop Dis. 2016 Jan; 10(1):e0004356. Long T, Neitz RJ, Beasley R, Kalyanaraman C, Suzuki BM, Jacobson MP, Dissous C, McKerrow JH, Drewry DH, Zuercher WJ, Singh R, Caffrey CR. PMID: 26751972.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    46. Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products. Future Med Chem. 2015; 7(16):2121-30. Ahlbach CL, Lexa KW, Bockus AT, Chen V, Crews P, Jacobson MP, Lokey RS. PMID: 26067057.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    47. Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides. Org Lett. 2015 Jun 19; 17(12):2928-31. 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. PMID: 26046483.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    48. 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. 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. PMID: 25950816.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    49. 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. Chow JY, Tian BX, Ramamoorthy G, Hillerich BS, Seidel RD, Almo SC, Jacobson MP, Poulter CD. PMID: 25901324.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    50. Synthesis and enzymatic studies of bisubstrate analogues for farnesyl diphosphate synthase. J Org Chem. 2015 Apr 17; 80(8):3902-13. Ramamoorthy G, Pugh ML, Tian BX, Phan RM, Perez LB, Jacobson MP, Poulter CD. PMID: 25734506.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    51. 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. Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJ. PMID: 25690569.
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    52. A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily. J Am Chem Soc. 2015 Feb 04; 137(4):1388-91. Zhang X, Kumar R, Vetting MW, Zhao S, Jacobson MP, Almo SC, Gerlt JA. PMID: 25608448.
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    53. 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. 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. PMID: 25540822.
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    54. Cell-permeable cyclic peptides from synthetic libraries inspired by natural products. J Am Chem Soc. 2015 Jan 21; 137(2):715-21. Hewitt WM, Leung SS, Pye CR, Ponkey AR, Bednarek M, Jacobson MP, Lokey RS. PMID: 25517352.
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    55. Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. PLoS Comput Biol. 2014 Oct; 10(10):e1003874. Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. PMID: 25299649.
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    56. 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. Hasnain S, McClendon CL, Hsu MT, Jacobson MP, Bandyopadhyay P. PMID: 25180859.
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    57. Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis. J Am Chem Soc. 2014 Sep 10; 136(36):12624-30. Krishnan S, Miller RM, Tian B, Mullins RD, Jacobson MP, Taunton J. PMID: 25153195.
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    58. A high throughput screen identifies potent and selective inhibitors to human epithelial 15-lipoxygenase-2. PLoS One. 2014; 9(8):e104094. Jameson JB, Kantz A, Schultz L, Kalyanaraman C, Jacobson MP, Maloney DJ, Jadhav A, Simeonov A, Holman TR. PMID: 25111178.
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    59. Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. Trends Biochem Sci. 2014 Aug; 39(8):363-71. Jacobson MP, Kalyanaraman C, Zhao S, Tian B. PMID: 24998033.
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    60. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30; 3. 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. PMID: 24980702.
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    61. Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58. Biochemistry. 2014 Jul 01; 53(25):4192-203. Groninger-Poe FP, Bouvier JT, Vetting MW, Kalyanaraman C, Kumar R, Almo SC, Jacobson MP, Gerlt JA. PMID: 24926996.
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    62. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model. 2014 Jun 23; 54(6):1687-99. Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. PMID: 24802635.
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    63. A structure-based model for predicting serum albumin binding. PLoS One. 2014; 9(4):e93323. Lexa KW, Dolghih E, Jacobson MP. PMID: 24691448.
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    64. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. mBio. 2014 Feb 11; 5(1):e00933-13. Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE. PMID: 24520058.
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    65. 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. Peng LX, Hsu MT, Bonomi M, Agard DA, Jacobson MP. PMID: 24516374.
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    66. 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. 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. PMID: 24530226.
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    67. SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. Cell Metab. 2013 Dec 03; 18(6):920-33. 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. PMID: 24315375.
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    68. A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection. Antimicrob Agents Chemother. 2013 Dec; 57(12):6063-73. Ndao M, Nath-Chowdhury M, Sajid M, Marcus V, Mashiyama ST, Sakanari J, Chow E, Mackey Z, Land KM, Jacobson MP, Kalyanaraman C, McKerrow JH, Arrowood MJ, Caffrey CR. PMID: 24060869.
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    69. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature. 2013 Oct 31; 502(7473):698-702. 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. PMID: 24056934.
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    70. Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells. Bioorg Med Chem. 2013 Dec 15; 21(24):7999-8012. Silber BM, Gever JR, Li Z, Gallardo-Godoy A, Renslo AR, Widjaja K, Irwin JJ, Rao S, Jacobson MP, Ghaemmaghami S, Prusiner SB. PMID: 24183589.
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    71. pH sensing by FAK-His58 regulates focal adhesion remodeling. J Cell Biol. 2013 Sep 16; 202(6):849-59. Choi CH, Webb BA, Chimenti MS, Jacobson MP, Barber DL. PMID: 24043700.
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    72. Biaryl amides and hydrazones as therapeutics for prion disease in transgenic mice. J Pharmacol Exp Ther. 2013 Nov; 347(2):325-38. 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. PMID: 23965382.
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    73. Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase. Biochemistry. 2013 Aug 20; 52(33):5511-3. Tian B, Wallrapp F, Kalyanaraman C, Zhao S, Eriksson LA, Jacobson MP. PMID: 23901785.
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    74. Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2. Structure. 2013 Sep 03; 21(9):1571-80. Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD. PMID: 23911090.
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    75. Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature. 2013 Jun 06; 498(7452):123-6. Kim J, Xiao H, Bonanno JB, Kalyanaraman C, Brown S, Tang X, Al-Obaidi NF, Patskovsky Y, Babbitt PC, Jacobson MP, Lee YS, Almo SC. PMID: 23676670.
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    76. 2-Aminothiazoles with improved pharmacotherapeutic properties for treatment of prion disease. ChemMedChem. 2013 May; 8(5):847-57. 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. PMID: 23509039.
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    77. 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. Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD. PMID: 23493556.
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    78. Considering protonation as a posttranslational modification regulating protein structure and function. Annu Rev Biophys. 2013; 42:289-314. Schönichen A, Webb BA, Jacobson MP, Barber DL. PMID: 23451893.
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    79. Pharmacokinetics and metabolism of 2-aminothiazoles with antiprion activity in mice. Pharm Res. 2013 Apr; 30(4):932-50. 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. PMID: 23417511.
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    80. Mephedrone (4-methylmethcathinone) supports intravenous self-administration in Sprague-Dawley and Wistar rats. Addict Biol. 2013 Sep; 18(5):786-99. Aarde SM, Angrish D, Barlow DJ, Wright MJ, Vandewater SA, Creehan KM, Houseknecht KL, Dickerson TJ, Taffe MA. PMID: 23386603.
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    81. Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein J Org Chem. 2013; 9:15-25. 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. PMID: 23400640.
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    82. 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. Spreafico M, Jacobson MP. PMID: 23578025.
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    83. Designing molecules to cross biological membranes. Curr Top Med Chem. 2013; 13(7):775. Lokey RS, Liras J, Liras S, Jacobson MP. PMID: 23578022.
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    84. 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. Dolghih E, Jacobson MP. PMID: 23421687.
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    85. Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. Structure. 2013 Jan 08; 21(1):54-64. Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJS, Jacobson MP, Kortemme T. PMID: 23159126.
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    86. Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance(). Medchemcomm. 2012 Oct; 3(10):1282-1289. 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. PMID: 23133740.
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    87. Computer-aided antibody design. Protein Eng Des Sel. 2012 Oct; 25(10):507-21. Kuroda D, Shirai H, Jacobson MP, Nakamura H. PMID: 22661385.
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    88. Testing physical models of passive membrane permeation. J Chem Inf Model. 2012 Jun 25; 52(6):1621-36. Leung SS, Mijalkovic J, Borrelli K, Jacobson MP. PMID: 22621168.
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    89. Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion. J Chem Theory Comput. 2012 Jul 12; 8(6):2115-2126. McClendon CL, Hua L, Barreiro A, Jacobson MP. PMID: 23316121.
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    90. Investigation of the proteolytic functions of an expanded cercarial elastase gene family in Schistosoma mansoni. PLoS Negl Trop Dis. 2012; 6(4):e1589. 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. PMID: 22509414.
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    91. 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):17050-17064. Kumar P, Chimenti MS, Pemble H, Schönichen A, Thompson O, Jacobson MP, Wittmann T. PMID: 22467876.
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    92. Predicting and improving the membrane permeability of peptidic small molecules. J Med Chem. 2012 Apr 12; 55(7):3163-9. Rafi SB, Hearn BR, Vedantham P, Jacobson MP, Renslo AR. PMID: 22394492.
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    93. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci U S A. 2012 Mar 13; 109(11):4122-7. Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. PMID: 22392983.
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    94. Phosphorylation of the Arp2 subunit relieves auto-inhibitory interactions for Arp2/3 complex activation. PLoS Comput Biol. 2011 Nov; 7(11):e1002226. Narayanan A, LeClaire LL, Barber DL, Jacobson MP. PMID: 22125478.
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    95. Divergent evolution in enolase superfamily: strategies for assigning functions. J Biol Chem. 2012 Jan 02; 287(1):29-34. Gerlt JA, Babbitt PC, Jacobson MP, Almo SC. PMID: 22069326.
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    96. The Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62. 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. PMID: 21999478.
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    97. On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds. Nat Chem Biol. 2011 Sep 25; 7(11):810-7. 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. PMID: 21946276.
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    98. Assessment of protein structure refinement in CASP9. Proteins. 2011; 79 Suppl 10:74-90. MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA. PMID: 22069034.
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    99. Dysregulated pH: a perfect storm for cancer progression. Nat Rev Cancer. 2011 08 11; 11(9):671-7. Webb BA, Chimenti M, Jacobson MP, Barber DL. PMID: 21833026.
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    100. A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series. J Chem Inf Model. 2011 Sep 26; 51(9):2082-9. Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP. PMID: 21780805.
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    101. Predicting binding to p-glycoprotein by flexible receptor docking. PLoS Comput Biol. 2011 Jun; 7(6):e1002083. Dolghih E, Bryant C, Renslo AR, Jacobson MP. PMID: 21731480.
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    102. A new view of the bacterial cytosol environment. PLoS Comput Biol. 2011 Jun; 7(6):e1002066. Cossins BP, Jacobson MP, Guallar V. PMID: 21695225.
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    103. Assessing protein loop flexibility by hierarchical Monte Carlo sampling. J Chem Theory Comput. 2011 May 10; 7(5):1564-1574. Nilmeier J, Hua L, Coutsias EA, Jacobson MP. PMID: 21743800.
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    104. 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. Sadowsky JD, Burlingame MA, Wolan DW, McClendon CL, Jacobson MP, Wells JA. PMID: 21430264.
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    105. Effects of somatic mutations on CDR loop flexibility during affinity maturation. Proteins. 2011 Mar; 79(3):821-9. Wong SE, Sellers BD, Jacobson MP. PMID: 21287614.
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    106. Modeling conformational ensembles of slow functional motions in Pin1-WW. PLoS Comput Biol. 2010 Dec 02; 6(12):e1001015. Morcos F, Chatterjee S, McClendon CL, Brenner PR, López-Rendón R, Zintsmaster J, Ercsey-Ravasz M, Sweet CR, Jacobson MP, Peng JW, Izaguirre JA. PMID: 21152000.
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    107. SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production. Cell Metab. 2010 Dec 01; 12(6):654-61. 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. PMID: 21109197.
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    108. Effects of somatic mutations on CDR loop flexibility during affinity maturation. Proteins. 2010 Oct 19. Wong SE, Sellers BD, Jacobson MP. PMID: 21136484.
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    109. Antibodies as a model system for comparative model refinement. Proteins. 2010 Aug 15; 78(11):2490-505. Sellers BD, Nilmeier JP, Jacobson MP. PMID: 20602354.
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    110. Conformation switching of clathrin light chain regulates clathrin lattice assembly. Dev Cell. 2010 May 18; 18(5):841-8. Wilbur JD, Hwang PK, Ybe JA, Lane M, Sellers BD, Jacobson MP, Fletterick RJ, Brodsky FM. PMID: 20493816.
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    111. Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway. Biochemistry. 2010 May 18; 49(19):4003-5. Kalyanaraman C, Jacobson MP. PMID: 20415432.
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    112. A nonazole CYP51 inhibitor cures Chagas' disease in a mouse model of acute infection. Antimicrob Agents Chemother. 2010 Jun; 54(6):2480-8. Doyle PS, Chen CK, Johnston JB, Hopkins SD, Leung SS, Jacobson MP, Engel JC, McKerrow JH, Podust LM. PMID: 20385875.
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    113. Binding-site assessment by virtual fragment screening. PLoS One. 2010 Apr 09; 5(4):e10109. Huang N, Jacobson MP. PMID: 20404926.
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    114. 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. Chen CK, Leung SS, Guilbert C, Jacobson MP, McKerrow JH, Podust LM. PMID: 20386598.
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    115. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis . Biochemistry. 2009 Dec 08; 48(48):11546-58. Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA. PMID: 19883118.
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    116. Automated site preparation in physics-based rescoring of receptor ligand complexes. Proteins. 2009 Oct; 77(1):52-61. Rapp CS, Schonbrun C, Jacobson MP, Kalyanaraman C, Huang N. PMID: 19382204.
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    117. Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. J Chem Theory Comput. 2009 Sep 08; 5(9):2486-2502. McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP. PMID: 20161451.
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    118. Monte Carlo Sampling with Hierarchical Move Sets: POSH Monte Carlo. J Chem Theory Comput. 2009 Aug 11; 5(8):1968-84. Nilmeier J, Jacobson MP. PMID: 26613140.
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    119. Improving the species cross-reactivity of an antibody using computational design. Bioorg Med Chem Lett. 2009 Jul 15; 19(14):3744-7. Farady CJ, Sellers BD, Jacobson MP, Craik CS. PMID: 19477127.
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    120. Computational studies of protein regulation by post-translational phosphorylation. Curr Opin Struct Biol. 2009 Apr; 19(2):156-63. Narayanan A, Jacobson MP. PMID: 19339172.
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    121. 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. Narayanan A, Sellers BD, Jacobson MP. PMID: 19324053.
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    122. 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. Tan ES, Naylor JC, Groban ES, Bunzow JR, Jacobson MP, Grandy DK, Scanlan TS. PMID: 19256523.
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    123. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009 Apr; 10(2):107-25. 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. PMID: 19219566.
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    124. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9. 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. PMID: 19217386.
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    125. Assessment of the protein-structure refinement category in CASP8. Proteins. 2009; 77 Suppl 9:66-80. MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. PMID: 19714776.
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    126. 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. Frantz C, Barreiro G, Dominguez L, Chen X, Eddy R, Condeelis J, Kelly MJ, Jacobson MP, Barber DL. PMID: 19029335.
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    127. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure. 2008 Nov 12; 16(11):1668-77. Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. PMID: 19000819.
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    128. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 2008 Aug 15; 72(3):959-71. Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. PMID: 18300241.
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    129. Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility. J Chem Theory Comput. 2008 May; 4(5):835-846. Nilmeier J, Jacobson M. PMID: 19119325.
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    130. Toward deciphering the code to aminergic G protein-coupled receptor drug design. Chem Biol. 2008 Apr; 15(4):343-53. Tan ES, Groban ES, Jacobson MP, Scanlan TS. PMID: 18420141.
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    131. Conformational selection in silico: loop latching motions and ligand binding in enzymes. Proteins. 2008 Apr; 71(1):153-64. Wong S, Jacobson MP. PMID: 17932934.
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    132. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol. 2008 Mar 28; 377(3):914-34. Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. PMID: 18280498.
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    133. An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. J Comput Aided Mol Des. 2007 Dec; 21(12):675-9. Kalyanaraman C, Jacobson MP. PMID: 17989930.
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    134. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol. 2007 Aug; 3(8):486-91. Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. PMID: 17603539.
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    135. Physics-based methods for studying protein-ligand interactions. Curr Opin Drug Discov Devel. 2007 May; 10(3):325-31. Huang N, Jacobson MP. PMID: 17554859.
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    136. 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 01; 66(4):824-37. Li X, Jacobson MP, Zhu K, Zhao S, Friesner RA. PMID: 17154422.
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    137. 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. Zhu K, Shirts MR, Friesner RA, Jacobson MP. PMID: 26637042.
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    138. Prediction of side-chain conformations on protein surfaces. Proteins. 2007 Mar 01; 66(4):814-23. Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B. PMID: 17206724.
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    139. Intracellular pH sensors: design principles and functional significance. Physiology (Bethesda). 2007 Feb; 22:30-9. Srivastava J, Barber DL, Jacobson MP. PMID: 17289928.
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    140. Strengths of hydrogen bonds involving phosphorylated amino acid side chains. J Am Chem Soc. 2007 Jan 31; 129(4):820-7. Mandell DJ, Chorny I, Groban ES, Wong SE, Levine E, Rapp CS, Jacobson MP. PMID: 17243818.
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    141. Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides. J Am Chem Soc. 2006 Nov 01; 128(43):14073-80. Rezai T, Bock JE, Zhou MV, Kalyanaraman C, Lokey RS, Jacobson MP. PMID: 17061890.
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    142. Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys. 2006 Nov 28; 8(44):5166-77. Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. PMID: 17203140.
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    143. 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. Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. PMID: 16740275.
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    144. Conformational changes in protein loops and helices induced by post-translational phosphorylation. PLoS Comput Biol. 2006 Apr; 2(4):e32. Groban ES, Narayanan A, Jacobson MP. PMID: 16628247.
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    145. Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers. J Am Chem Soc. 2006 Mar 01; 128(8):2510-1. Rezai T, Yu B, Millhauser GL, Jacobson MP, Lokey RS. PMID: 16492015.
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    146. Novel human lipoxygenase inhibitors discovered using virtual screening with homology models. J Med Chem. 2006 Feb 23; 49(4):1356-63. Kenyon V, Chorny I, Carvajal WJ, Holman TR, Jacobson MP. PMID: 16480270.
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    147. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem. 2006 Jan 26; 49(2):534-53. Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. PMID: 16420040.
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    148. 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. Yu Z, Jacobson MP, Friesner RA. PMID: 16261581.
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    149. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. J Chem Inf Model. 2006 Jan-Feb; 46(1):243-53. Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. PMID: 16426060.
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    150. Surfaces affect ion pairing. J Phys Chem B. 2005 Dec 22; 109(50):24056-60. Chorny I, Dill KA, Jacobson MP. PMID: 16375397.
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    151. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods. J Biomol Screen. 2005 Oct; 10(7):675-81. Bernacki K, Kalyanaraman C, Jacobson MP. PMID: 16170049.
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    152. 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. Wong SE, Bernacki K, Jacobson M. PMID: 16863191.
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    153. Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry. 2005 Feb 15; 44(6):2059-71. Kalyanaraman C, Bernacki K, Jacobson MP. PMID: 15697231.
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    154. Tryptophan 500 and arginine 707 define product and substrate active site binding in soybean lipoxygenase-1. Biochemistry. 2004 Oct 19; 43(41):13063-71. Ruddat VC, Mogul R, Chorny I, Chen C, Perrin N, Whitman S, Kenyon V, Jacobson MP, Bernasconi CF, Holman TR. PMID: 15476400.
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    155. A hierarchical approach to all-atom protein loop prediction. Proteins. 2004 May 01; 55(2):351-67. Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. PMID: 15048827.
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    156. High-resolution prediction of protein helix positions and orientations. Proteins. 2004 May 01; 55(2):368-82. Li X, Jacobson MP, Friesner RA. PMID: 15048828.
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    157. A kinematic view of loop closure. J Comput Chem. 2004 Mar; 25(4):510-28. Coutsias EA, Seok C, Jacobson MP, Dill KA. PMID: 14735570.
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    158. Cognition and anatomy in three variants of primary progressive aphasia. Ann Neurol. 2004 Mar; 55(3):335-46. Gorno-Tempini ML, Dronkers NF, Rankin KP, Ogar JM, Phengrasamy L, Rosen HJ, Johnson JK, Weiner MW, Miller BL. PMID: 15001364.
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    159. On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol. 2002 Jul 12; 320(3):597-608. Jacobson MP, Friesner RA, Xiang Z, Honig B. PMID: 12096912.
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    160. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. J Struct Funct Genomics. 2002; 2(2):103-11. Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM. PMID: 12836667.
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    161. Journal of Chemical Physics. Unexpected Simplicity in the S1 -> S0 Dispersed Fluorescence Spectrum of 13C2H2. 2002; 16:7939–7947. Silva ML, Jacobson MP, Duan Z, and Field RW.
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