Matt Jacobson, PhD

Title(s)Professor, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address1700 4th St, #408E
San Francisco CA 94158
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 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. Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma. Clin Cancer Res. 2023 11 14; 29(22):4613-4626. Paolino J, Dimitrov B, Apsel Winger B, Sandoval-Perez A, Rangarajan AV, Ocasio-Martinez N, Tsai HK, Li Y, Robichaud AL, Khalid D, Hatton C, Gillani R, Polonen P, Dilig A, Gotti G, Kavanagh J, Adhav AA, Gow S, Tsai J, Li Y, Ebert BL, Van Allen EM, Bledsoe J, Kim AS, Tasian SK, Cooper SL, Cooper TM, Hijiya N, Sulis ML, Shukla NN, Magee JA, Mullighan CG, Burke MJ, Luskin MR, Mar BG, Jacobson MP, Harris MH, Stegmaier K, Place AE, Pikman Y. PMID: 37725576; PMCID: PMC10872648.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    2. Searching for molecular hypoxia sensors among oxygen-dependent enzymes. Elife. 2023 07 26; 12. Li L, Shen S, Bickler P, Jacobson MP, Wu LF, Altschuler SJ. PMID: 37494095; PMCID: PMC10371230.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    3. Correction: Mutations in α-synuclein, TDP-43 and tau prolong protein half-life through diminished degradation by lysosomal proteases. Mol Neurodegener. 2023 May 30; 18(1):34. Sampognaro PJ, Arya S, Knudsen GM, Gunderson EL, Sandoval-Perez A, Hodul M, Bowles K, Craik CS, Jacobson MP, Kao AW. PMID: 37254128; PMCID: PMC10228009.
      View in: PubMed   Mentions:    Fields:    
    4. Signal peptide mimicry primes Sec61 for client-selective inhibition. Nat Chem Biol. 2023 09; 19(9):1054-1062. Rehan S, Tranter D, Sharp PP, Craven GB, Lowe E, Anderl JL, Muchamuel T, Abrishami V, Kuivanen S, Wenzell NA, Jennings A, Kalyanaraman C, Strandin T, Javanainen M, Vapalahti O, Jacobson MP, McMinn D, Kirk CJ, Huiskonen JT, Taunton J, Paavilainen VO. PMID: 37169961; PMCID: PMC10449633.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    5. Dissecting the effects of GTPase and kinase domain mutations on LRRK2 endosomal localization and activity. Cell Rep. 2023 05 30; 42(5):112447. Rinaldi C, Waters CS, Li Z, Kumbier K, Rao L, Nichols RJ, Jacobson MP, Wu LF, Altschuler SJ. PMID: 37141099.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    6. Mutations in α-synuclein, TDP-43 and tau prolong protein half-life through diminished degradation by lysosomal proteases. Mol Neurodegener. 2023 05 02; 18(1):29. Sampognaro PJ, Arya S, Knudsen GM, Gunderson EL, Sandoval-Perez A, Hodul M, Bowles K, Craik CS, Jacobson MP, Kao AW. PMID: 37131250; PMCID: PMC10155372.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    7. Correction to "Assessing the Activation of Tyrosine Kinase KIT through Free Energy Calculations". J Chem Theory Comput. 2022 Dec 09. Sandoval-Pérez A, Winger BA, Jacobson MP. PMID: 36493348.
      View in: PubMed   Mentions:    Fields:    
    8. Fighting Plasmodium chloroquine resistance with acetylenic chloroquine analogues. Int J Parasitol Drugs Drug Resist. 2022 Oct 31; 20:121-128. Cortopassi WA, Gunderson E, Annunciato Y, Silva AES, Dos Santos Ferreira A, Garcia Teles CB, Pimentel AS, Ramamoorthi R, Gazarini ML, Meneghetti MR, Guido RVC, Pereira DB, Jacobson MP, Krettli AU, Caroline C Aguiar A. PMID: 36375339.
      View in: PubMed   Mentions:    Fields:    
    9. Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor. Science. 2022 09 30; 377(6614):eabn7065. Fink EA, Xu J, Hübner H, Braz JM, Seemann P, Avet C, Craik V, Weikert D, Schmidt MF, Webb CM, Tolmachova NA, Moroz YS, Huang XP, Kalyanaraman C, Gahbauer S, Chen G, Liu Z, Jacobson MP, Irwin JJ, Bouvier M, Du Y, Shoichet BK, Basbaum AI, Gmeiner P. PMID: 36173843; PMCID: PMC10360211.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimals
    10. Assessing the Activation of Tyrosine Kinase KIT through Free Energy Calculations. J Chem Theory Comput. 2022 Oct 11; 18(10):6251-6258. Sandoval-Pérez A, Winger BA, Jacobson MP. PMID: 36166736; PMCID: PMC9558371.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    11. Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation. Biochemistry. 2022 Oct 18; 61(20):2165-2176. Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP. PMID: 36161872; PMCID: PMC9583617.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    12. Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters. Sci Adv. 2022 01 28; 8(4):eabi7711. Sun X, Bieber JM, Hammerlindl H, Chalkley RJ, Li KH, Burlingame AL, Jacobson MP, Wu LF, Altschuler SJ. PMID: 35089788; PMCID: PMC8797778.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    13. Kinetic and structural investigations of novel inhibitors of human epithelial 15-lipoxygenase-2. Bioorg Med Chem. 2021 09 15; 46:116349. Tsai WC, Gilbert NC, Ohler A, Armstrong M, Perry S, Kalyanaraman C, Yasgar A, Rai G, Simeonov A, Jadhav A, Standley M, Lee HW, Crews P, Iavarone AT, Jacobson MP, Neau DB, Offenbacher AR, Newcomer M, Holman TR. PMID: 34500187; PMCID: PMC8785688.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    14. Docking and mutagenesis studies lead to improved inhibitor development of ML355 for human platelet 12-lipoxygenase. Bioorg Med Chem. 2021 09 15; 46:116347. Tsai WC, Aleem AM, Tena J, Rivera-Velazquez M, Brah HS, Tripathi S, D'silva M, Nadler JL, Kalyanaraman C, Jacobson MP, Holman T. PMID: 34507163.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    15. Analogs of the Dopamine Metabolite 5,6-Dihydroxyindole Bind Directly to and Activate the Nuclear Receptor Nurr1. ACS Chem Biol. 2021 07 16; 16(7):1159-1163. Kholodar SA, Lang G, Cortopassi WA, Iizuka Y, Brah HS, Jacobson MP, England PM. PMID: 34165961; PMCID: PMC9064169.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    16. 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 06 08; 60(22):1741-1754. Tsai WC, Kalyanaraman C, Yamaguchi A, Holinstat M, Jacobson MP, Holman TR. PMID: 34029049; PMCID: PMC9007043.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    17. Protomer alignment modulates specificity of RNA substrate recognition by Ire1. Elife. 2021 04 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; PMCID: PMC8104961.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    18. Gasdermin D pore structure reveals preferential release of mature interleukin-1. Nature. 2021 05; 593(7860):607-611. Xia S, Zhang Z, Magupalli VG, Pablo JL, Dong Y, Vora SM, Wang L, Fu TM, Jacobson MP, Greka A, Lieberman J, Ruan J, Wu H. PMID: 33883744; PMCID: PMC8588876.
      View in: PubMed   Mentions: 191     Fields:    Translation:HumansAnimalsCells
    19. 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; PMCID: PMC8035302.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    20. 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: 2     Fields:    Translation:HumansCells
    21. Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium. Cancer Discov. 2021 06; 11(6):1424-1439. Pikman Y, Tasian SK, Sulis ML, Stevenson K, Blonquist TM, Apsel Winger B, Cooper TM, Pauly M, Maloney KW, Burke MJ, Brown PA, Gossai N, McNeer JL, Shukla NN, Cole PD, Kahn JM, Chen J, Barth MJ, Magee JA, Gennarini L, Adhav AA, Clinton CM, Ocasio-Martinez N, Gotti G, Li Y, Lin S, Imamovic A, Tognon CE, Patel T, Faust HL, Contreras CF, Cremer A, Cortopassi WA, Garrido Ruiz D, Jacobson MP, Dharia NV, Su A, Robichaud AL, Saur Conway A, Tarlock K, Stieglitz E, Place AE, Puissant A, Hunger SP, Kim AS, Lindeman NI, Gore L, Janeway KA, Silverman LB, Tyner JW, Harris MH, Loh ML, Stegmaier K. PMID: 33563661; PMCID: PMC8178162.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCTClinical Trials
    22. Synthesis and Screening of α-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; PMCID: PMC8483608.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    23. 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; PMCID: PMC7721368.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    24. 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; PMCID: PMC7546582.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
    25. The Synthesis and Structural Requirements for Measuring Glucocorticoid Receptor Expression In Vivo with (±)-11C-YJH08 PET. J Nucl Med. 2021 05 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; PMCID: PMC8844266.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    26. 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; PMCID: PMC7328043.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    27. 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; PMCID: PMC7729281.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    28. 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; PMCID: PMC7431030.
      View in: PubMed   Mentions: 2284     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    29. 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; PMCID: PMC7239059.
      View in: PubMed   Mentions: 28  
    30. 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; PMCID: PMC6703691.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    31. ATP-Competitive Inhibitors Midostaurin and Avapritinib Have Distinct Resistance Profiles in Exon 17-Mutant KIT. Cancer Res. 2019 08 15; 79(16):4283-4292. Apsel Winger B, Cortopassi WA, Garrido Ruiz D, Ding L, Jang K, Leyte-Vidal A, Zhang N, Esteve-Puig R, Jacobson MP, Shah NP. PMID: 31270078; PMCID: PMC6697585.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    32. 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; PMCID: PMC6666309.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    33. 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; PMCID: PMC6588463.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    34. 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; PMCID: PMC6552421.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    35. 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; PMCID: PMC6486493.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    36. Structure-based identification of novel CK2 inhibitors with a linear 2-propenone scaffold as anti-cancer agents. Biochem Biophys Res Commun. 2019 04 30; 512(2):208-212. Qi X, Zhang N, Zhao L, Hu L, Cortopassi WA, Jacobson MP, Li X, Zhong R. PMID: 30878184.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    37. 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; PMCID: PMC7185887.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    38. 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; PMCID: PMC6613950.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    39. 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; PMCID: PMC7270147.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    40. 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; PMCID: PMC6286348.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    41. Structure-based Discovery of Novel CK2α-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
    42. 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; PMCID: PMC6104643.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansAnimalsCells
    43. 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; PMCID: PMC5824822.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    44. 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; PMCID: PMC5857975.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
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    50. 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; PMCID: PMC5570307.
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    51. Synthesis of the Ca2+-mobilizing messengers NAADP and cADPR by intracellular CD38 enzyme in the mouse heart: Role in β-adrenoceptor signaling. J Biol Chem. 2017 08 11; 292(32):13243-13257. Lin WK, Bolton EL, Cortopassi WA, Wang Y, O'Brien F, Maciejewska M, Jacobson MP, Garnham C, Ruas M, Parrington J, Lei M, Sitsapesan R, Galione A, Terrar DA. PMID: 28539361; PMCID: PMC5555186.
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    53. 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; PMCID: PMC5346980.
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    70. 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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    108. 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; PMCID: PMC3538811.
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    109. 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; PMCID: PMC3317910.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    110. 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; PMCID: PMC3366819.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    111. 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; PMCID: PMC3325374.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    112. 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; PMCID: PMC3306705.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    113. 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; PMCID: PMC3220268.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    114. 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; PMCID: PMC3249080.
      View in: PubMed   Mentions: 58     Fields:    Translation:Humans
    115. 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; PMCID: PMC3238057.
      View in: PubMed   Mentions: 96     Fields:    Translation:HumansAnimalsCells
    116. 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; PMCID: PMC3210067.
      View in: PubMed   Mentions: 91     Fields:    Translation:AnimalsCells
    117. 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; PMCID: PMC3238793.
      View in: PubMed   Mentions: 57     Fields:    Translation:Cells
    118. 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.
      View in: PubMed   Mentions: 683     Fields:    Translation:Humans
    119. 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; PMCID: PMC3183355.
      View in: PubMed   Mentions: 15     Fields:    
    120. 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; PMCID: PMC3121697.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    121. A new view of the bacterial cytosol environment. PLoS Comput Biol. 2011 Jun; 7(6):e1002066. Cossins BP, Jacobson MP, Guallar V. PMID: 21695225; PMCID: PMC3111478.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    122. 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; PMCID: PMC3129859.
      View in: PubMed   Mentions: 8     Fields:    
    123. 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; PMCID: PMC3076885.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    124. 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.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    125. 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; PMCID: PMC2996313.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    126. 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; PMCID: PMC3310379.
      View in: PubMed   Mentions: 253     Fields:    Translation:AnimalsCells
    127. Effects of somatic mutations on CDR loop flexibility during affinity maturation. Proteins. 2010 Oct 19. Wong SE, Sellers BD, Jacobson MP. PMID: 21136484.
      View in: PubMed   Mentions:
    128. 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; PMCID: PMC2998178.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    129. 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; PMCID: PMC2975025.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
    130. 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; PMCID: PMC2877507.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    131. 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; PMCID: PMC2876414.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    132. Binding-site assessment by virtual fragment screening. PLoS One. 2010 Apr 09; 5(4):e10109. Huang N, Jacobson MP. PMID: 20404926; PMCID: PMC2852417.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    133. 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; PMCID: PMC2850312.
      View in: PubMed   Mentions: 61     Fields:    Translation:AnimalsCells
    134. 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; PMCID: PMC2787699.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    135. 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; PMCID: PMC2744578.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    136. 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; PMCID: PMC2790287.
      View in: PubMed   Mentions: 103     Fields:    
    137. 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.
      View in: PubMed   Mentions: 3     Fields:    
    138. 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; PMCID: PMC2724971.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    139. 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.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    140. 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.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    141. 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; PMCID: PMC2677188.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    142. 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; PMCID: PMC2693957.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    143. 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; PMCID: PMC2739730.
      View in: PubMed   Mentions: 81     Fields:    Translation:HumansAnimalsCells
    144. 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; PMCID: PMC2801025.
      View in: PubMed   Mentions: 46     Fields:    Translation:Cells
    145. 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; PMCID: PMC2592832.
      View in: PubMed   Mentions: 101     Fields:    Translation:HumansAnimalsCells
    146. 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; PMCID: PMC2714228.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    147. 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; PMCID: PMC2764870.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    148. 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; PMCID: PMC2612633.
      View in: PubMed   Mentions: 3     Fields:    
    149. 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; PMCID: PMC2713717.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    150. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    151. 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; PMCID: PMC2752715.
      View in: PubMed   Mentions: 71     Fields:    Translation:Cells
    152. An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. J Comput Aided Mol Des. 2007 Dec; 21(12):675-9. Kalyanaraman C, Jacobson MP. PMID: 17989930.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    153. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol. 2007 Aug; 3(8):486-91. Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. PMID: 17603539.
      View in: PubMed   Mentions: 51     Fields:    Translation:Cells
    154. 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.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    155. 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.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    156. 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.
      View in: PubMed   Mentions: 17     Fields:    
    157. 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; PMCID: PMC2743384.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    158. Intracellular pH sensors: design principles and functional significance. Physiology (Bethesda). 2007 Feb; 22:30-9. Srivastava J, Barber DL, Jacobson MP. PMID: 17289928.
      View in: PubMed   Mentions: 83     Fields:    Translation:HumansAnimalsCells
    159. 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.
      View in: PubMed   Mentions: 51     Fields:    Translation:Cells
    160. Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides. J Am Chem Soc. 2006 Nov 01; 128(43):14073-80. Rezai T, Bock JE, Zhou MV, Kalyanaraman C, Lokey RS, Jacobson MP. PMID: 17061890.
      View in: PubMed   Mentions: 108     Fields:    Translation:Cells
    161. Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys. 2006 Nov 28; 8(44):5166-77. Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. PMID: 17203140.
      View in: PubMed   Mentions: 50     Fields:    Translation:Cells
    162. 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.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    163. 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; PMCID: PMC1440919.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansAnimalsCells
    164. 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.
      View in: PubMed   Mentions: 130     Fields:    Translation:Cells
    165. 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.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    166. 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.
      View in: PubMed   Mentions: 621     Fields:    Translation:Cells
    167. 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; PMCID: PMC2743414.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    168. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. J Chem Inf Model. 2006 Jan-Feb; 46(1):243-53. Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. PMID: 16426060.
      View in: PubMed   Mentions: 49     Fields:    Translation:Cells
    169. Surfaces affect ion pairing. J Phys Chem B. 2005 Dec 22; 109(50):24056-60. Chorny I, Dill KA, Jacobson MP. PMID: 16375397.
      View in: PubMed   Mentions: 23     Fields:    
    170. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods. J Biomol Screen. 2005 Oct; 10(7):675-81. Bernacki K, Kalyanaraman C, Jacobson MP. PMID: 16170049.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    171. 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.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    172. Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry. 2005 Feb 15; 44(6):2059-71. Kalyanaraman C, Bernacki K, Jacobson MP. PMID: 15697231.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    173. 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.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    174. 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.
      View in: PubMed   Mentions: 783     Fields:    Translation:Cells
    175. 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.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    176. Computational modeling of the catalytic reaction in triosephosphate isomerase. J Mol Biol. 2004 Mar 12; 337(1):227-39. Guallar V, Jacobson M, McDermott A, Friesner RA. PMID: 15001364.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    177. 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.
      View in: PubMed   Mentions: 96     Fields:    
    178. 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.
      View in: PubMed   Mentions: 431     Fields:    Translation:Cells
    179. 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.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    180. 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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