Matt Jacobson, PhD

Professor
Department of Pharmaceutical Chemistry
[email protected]
1700 4th Street, Rm 408E
UCSF Box 2540
San Francisco, CA 94158
United States

Links

Jacobson Lab UCSF Profiles

Affiliations

Education programs

Associate Director, Quantitative Biosciences Consortium (QBC)
Biophysics Graduate Program (BP)
Biological and Medical Informatics Graduate Program (BMI)
Chemistry and Chemical Biology Graduate Program (CCB)

UCSF centers, institutes, and research programs

Quantitative Biosciences Institute (QBI)

What I do

Research in my lab focuses on atomic-level mechanisms of protein regulation, protein-ligand interactions, and computer-aided drug design. My approach is to employ physics-based energy models for predictive protein modeling. Projects in my lab combine algorithm development and biological applications.

Departmental research area

computational biology and chemistry

My research expertise

computer-aided drug design, allostery, post-translational protein modification, protein structure and dynamics

Professional background

Degrees

PhD, Physical Chemistry, Massachusetts Institute of Technology (MIT), 1999
BS, Chemistry, Stanford University, 1993

Biography

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

Research keywords

  • Lipoxygenase Inhibitors
  • computational biology
  • Piebaldism
  • Molecular Docking Simulation
  • Enzymes
  • Computer Simulation
  • Protein Conformation
  • Arachidonate 12-Lipoxygenase
  • Molecular Dynamics Simulation
  • Molecular Models
  • Phosphopyruvate Hydratase
  • proteins
  • Alkyl and Aryl Transferases
  • Arachidonate 15-Lipoxygenase
  • Cell Membrane Permeability
1. Closing the equity gap in science
2. Helium recycling project sets a new standard for sustainability at UCSF
3. Update from the Dean: Recovery and resilience after a pandemic year
4. Jacobson’s story of battling illness while teaching featured in UCSF Magazine
5. Arkin named next chair of Department of Pharmaceutical Chemistry
6. Update from the Dean: Confronting racism and health inequities
7. Update from the Dean – November 2019
8. VR drug discovery makes precision therapy a reality
9. 2019 Koda-Kimble Seed Award supports School of Pharmacy’s boldest ideas
10. The epic journey to better medicines
11. Prien and MacWilliam bequests establish new endowed professorships
12. Shoichet receives DeLano Award for Computational Biosciences
13. Celebrating the 100th birthday of Edward Leong Way
14. Update from the Dean - Fall/Winter 2015
15. Jacobson named chair of the Department of Pharmaceutical Chemistry
16. Update from the Dean - Spring/Summer 2015
17. Innovation in Education Awards go to Shin, Jacobson, Ferrone
18. Update from the Dean - Spring/Summer 2011
19. Reflection: 30 years of top NIH funding for UCSF School of Pharmacy
20. Two to watch
21. Update from the Dean - July 2004
22. Jacobson receives Sloan Fellowship
23. About Leslie Wilson, and more news
1. UCSF School of Pharmacy Dean’s Recognition for Excellence in Teaching, 2006
2. Alfred P. Sloan Research Fellowship, 2004
3. NSF CAREER Award, 2004
4. National Science Foundation Postdoctoral Fellowship in Biological Informatics, 2000-2002
5. Air Force Research Laboratory, Space Vehicles Directorate “Team Publication of the Year Award”, 2000
6. EPSRC (Engineering and Physical Sciences Research Council, U.K.) Visiting Fellow, 1999-2000
7. Fannie and John Hertz Fellow, 1998-1999
8. Rao Prize, for “outstanding student talk” at the International Symposium on Molecular Spectroscopy, Ohio State University, 1997
9. National Defense Science and Engineering Graduate Fellow, 1995-1998
10. American Institute of Chemists Graduation Award, Stanford University, 1993
11. Phi Beta Kappa, Stanford University, 1993
12. David Starr Jordan Scholar, Stanford University, 1989

Publications

Leyte-Vidal A, Garrido Ruiz D, DeFilippis R, Leske IB, Rea D, Phan S, Miller KB, Hu F, Mase A, Shan Y, Hantschel O, Jacobson MP, Shah NP. BCR::ABL1 kinase N-lobe mutants confer moderate to high degrees of resistance to asciminib. Blood. 2024 Aug 08; 144(6):639-645.
Kumbier K, Roth M, Li Z, Lazzari-Dean J, Waters C, Hammerlindl S, Rinaldi C, Huang P, Korobeynikov VA, New York Genome Center ALS Consortium, Phatnani H, Shneider N, Jacobson MP, Wu LF, Altschuler SJ. Identifying FUS amyotrophic lateral sclerosis disease signatures in patient dermal fibroblasts. Dev Cell. 2024 Aug 19; 59(16):2134-2142.e6.
Kisor KP, Ruiz DG, Jacobson MP, Barber DL. A role for pH dynamics regulating transcription factor DNA binding selectivity. bioRxiv. 2024 May 21.
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. 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.
Li L, Shen S, Bickler P, Jacobson MP, Wu LF, Altschuler SJ. Searching for molecular hypoxia sensors among oxygen-dependent enzymes. Elife. 2023 07 26; 12.
Sampognaro PJ, Arya S, Knudsen GM, Gunderson EL, Sandoval-Perez A, Hodul M, Bowles K, Craik CS, Jacobson MP, Kao AW. 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.
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. Signal peptide mimicry primes Sec61 for client-selective inhibition. Nat Chem Biol. 2023 09; 19(9):1054-1062.
Rinaldi C, Waters CS, Li Z, Kumbier K, Rao L, Nichols RJ, Jacobson MP, Wu LF, Altschuler SJ. Dissecting the effects of GTPase and kinase domain mutations on LRRK2 endosomal localization and activity. Cell Rep. 2023 05 30; 42(5):112447.
Sampognaro PJ, Arya S, Knudsen GM, Gunderson EL, Sandoval-Perez A, Hodul M, Bowles K, Craik CS, Jacobson MP, Kao AW. 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.
Sandoval-Pérez A, Winger BA, Jacobson MP. Correction to "Assessing the Activation of Tyrosine Kinase KIT through Free Energy Calculations". J Chem Theory Comput. 2023 Jan 10; 19(1):376.
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. Fighting Plasmodium chloroquine resistance with acetylenic chloroquine analogues. Int J Parasitol Drugs Drug Resist. 2022 Dec; 20:121-128.
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. Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor. Science. 2022 09 30; 377(6614):eabn7065.
Sandoval-Pérez A, Winger BA, Jacobson MP. Assessing the Activation of Tyrosine Kinase KIT through Free Energy Calculations. J Chem Theory Comput. 2022 Oct 11; 18(10):6251-6258.
Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP. Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation. Biochemistry. 2022 10 18; 61(20):2165-2176.
Sun X, Bieber JM, Hammerlindl H, Chalkley RJ, Li KH, Burlingame AL, Jacobson MP, Wu LF, Altschuler SJ. Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters. Sci Adv. 2022 01 28; 8(4):eabi7711.
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. Kinetic and structural investigations of novel inhibitors of human epithelial 15-lipoxygenase-2. Bioorg Med Chem. 2021 09 15; 46:116349.
Tsai WC, Aleem AM, Tena J, Rivera-Velazquez M, Brah HS, Tripathi S, D'silva M, Nadler JL, Kalyanaraman C, Jacobson MP, Holman T. Docking and mutagenesis studies lead to improved inhibitor development of ML355 for human platelet 12-lipoxygenase. Bioorg Med Chem. 2021 09 15; 46:116347.
Kholodar SA, Lang G, Cortopassi WA, Iizuka Y, Brah HS, Jacobson MP, England PM. 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.
Tsai WC, Kalyanaraman C, Yamaguchi A, Holinstat M, Jacobson MP, Holman TR. 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.
Li W, Crotty K, Garrido Ruiz D, Voorhies M, Rivera C, Sil A, Mullins RD, Jacobson MP, Peschek J, Walter P. Protomer alignment modulates specificity of RNA substrate recognition by Ire1. Elife. 2021 04 27; 10.
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. Gasdermin D pore structure reveals preferential release of mature interleukin-1. Nature. 2021 05; 593(7860):607-611.
Lak P, O'Donnell H, Du X, Jacobson MP, Shoichet BK. A Crowding Barrier to Protein Inhibition in Colloidal Aggregates. J Med Chem. 2021 04 08; 64(7):4109-4116.
Tsai WC, Aleem AM, Whittington C, Cortopassi WA, Kalyanaraman C, Baroz A, Iavarone AT, Skrzypczak-Jankun E, Jacobson MP, Offenbacher AR, Holman T. Mutagenesis, Hydrogen-Deuterium Exchange, and Molecular Docking Investigations Establish the Dimeric Interface of Human Platelet-Type 12-Lipoxygenase. Biochemistry. 2021 03 16; 60(10):802-812.
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. 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.
Kalita M, Villanueva-Meyer J, Ohkawa Y, Kalyanaraman C, Chen K, Mohamed E, Parker MFL, Jacobson MP, Phillips JJ, Evans MJ, Wilson DM. Synthesis and Screening of α-Xylosides in Human Glioblastoma Cells. Mol Pharm. 2021 01 04; 18(1):451-460.
Perry SC, Horn T, Tourdot BE, Yamaguchi A, Kalyanaraman C, Conrad WS, Akinkugbe O, Holinstat M, Jacobson MP, Holman TR. Role of Human 15-Lipoxygenase-2 in the Biosynthesis of the Lipoxin Intermediate, 5S,15S-diHpETE, Implicated with the Altered Positional Specificity of Human 15-Lipoxygenase-1. Biochemistry. 2020 10 27; 59(42):4118-4130.
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. Synthetic group A streptogramin antibiotics that overcome Vat resistance. Nature. 2020 10; 586(7827):145-150.
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. 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.
Perry SC, Kalyanaraman C, Tourdot BE, Conrad WS, Akinkugbe O, Freedman JC, Holinstat M, Jacobson MP, Holman TR. 15-Lipoxygenase-1 biosynthesis of 7S,14S-diHDHA implicates 15-lipoxygenase-2 in biosynthesis of resolvin D5. J Lipid Res. 2020 07; 61(7):1087-1103.
Freedman C, Tran A, Tourdot BE, Kalyanaraman C, Perry S, Holinstat M, Jacobson MP, Holman TR. Biosynthesis of the Maresin Intermediate, 13S,14S-Epoxy-DHA, by Human 15-Lipoxygenase and 12-Lipoxygenase and Its Regulation through Negative Allosteric Modulators. Biochemistry. 2020 05 19; 59(19):1832-1844.
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. 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, 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. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 22.
Butler VJ, Gao F, Corrales CI, Cortopassi WA, Caballero B, Vohra M, Ashrafi K, Cuervo AM, Jacobson MP, Coppola G, Kao AW. 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.
Apsel Winger B, Cortopassi WA, Garrido Ruiz D, Ding L, Jang K, Leyte-Vidal A, Zhang N, Esteve-Puig R, Jacobson MP, Shah NP. ATP-Competitive Inhibitors Midostaurin and Avapritinib Have Distinct Resistance Profiles in Exon 17-Mutant KIT. Cancer Res. 2019 08 15; 79(16):4283-4292.
Butler VJ, Cortopassi WA, Gururaj S, Wang AL, Pierce OM, Jacobson MP, Kao AW. 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.
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. Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. Mol Cell. 2019 06 20; 74(6):1164-1174.e4.
Charafeddine RA, Cortopassi WA, Lak P, Tan R, McKenney RJ, Jacobson MP, Barber DL, Wittmann T. 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.
Ball KA, Chan LM, Stanley DJ, Tierney E, Thapa S, Ta HM, Burton L, Binning JM, Jacobson MP, Gross JD. Conformational Dynamics of the HIV-Vif Protein Complex. Biophys J. 2019 04 23; 116(8):1432-1445.
Qi X, Zhang N, Zhao L, Hu L, Cortopassi WA, Jacobson MP, Li X, Zhong R. 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.
Bruning JM, Wang Y, Oltrabella F, Tian B, Kholodar SA, Liu H, Bhattacharya P, Guo S, Holton JM, Fletterick RJ, Jacobson MP, England PM. Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite. Cell Chem Biol. 2019 05 16; 26(5):674-685.e6.
Butler VJ, Cortopassi WA, Argouarch AR, Ivry SL, Craik CS, Jacobson MP, Kao AW. Progranulin Stimulates the In Vitro Maturation of Pro-Cathepsin D at Acidic pH. J Mol Biol. 2019 03 01; 431(5):1038-1047.
Aleem AM, Tsai WC, Tena J, Alvarez G, Deschamps J, Kalyanaraman C, Jacobson MP, Holman T. Probing the Electrostatic and Steric Requirements for Substrate Binding in Human Platelet-Type 12-Lipoxygenase. Biochemistry. 2019 02 12; 58(6):848-857.
Bisignano P, Ghezzi C, Jo H, Polizzi NF, Althoff T, Kalyanaraman C, Friemann R, Jacobson MP, Wright EM, Grabe M. Inhibitor binding mode and allosteric regulation of Na+-glucose symporters. Nat Commun. 2018 12 07; 9(1):5245.
Tang S, Zhang N, Zhou Y, Cortopassi WA, Jacobson MP, Zhao LJ, Zhong RG. Structure-based Discovery of Novel CK2α-Binding Cyclic Peptides with Anti-cancer Activity. Mol Inform. 2019 03; 38(3):e1800089.
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. 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.
Goode B, Mondal G, Hyun M, Ruiz DG, Lin YH, Van Ziffle J, Joseph NM, Onodera C, Talevich E, Grenert JP, Hewedi IH, Snuderl M, Brat DJ, Kleinschmidt-DeMasters BK, Rodriguez FJ, Louis DN, Yong WH, Lopes MB, Rosenblum MK, Butowski N, Tihan T, Bollen AW, Phillips JJ, Wiita AP, Yeh I, Jacobson MP, Bastian BC, Perry A, Solomon DA. A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle. Nat Commun. 2018 02 23; 9(1):810.
Taylor IR, Dunyak BM, Komiyama T, Shao H, Ran X, Assimon VA, Kalyanaraman C, Rauch JN, Jacobson MP, Zuiderweg ERP, Gestwicki JE. High-throughput screen for inhibitors of protein-protein interactions in a reconstituted heat shock protein 70 (Hsp70) complex. J Biol Chem. 2018 03 16; 293(11):4014-4025.
Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A. Prediction of enzymatic pathways by integrative pathway mapping. Elife. 2018 01 29; 7.
de Jesus Cortez F, Nguyen P, Truillet C, Tian B, Kuchenbecker KM, Evans MJ, Webb P, Jacobson MP, Fletterick RJ, England PM. Development of 5N-Bicalutamide, a High-Affinity Reversible Covalent Antiandrogen. ACS Chem Biol. 2017 12 15; 12(12):2934-2939.
Hindle SJ, Munji RN, Dolghih E, Gaskins G, Orng S, Ishimoto H, Soung A, DeSalvo M, Kitamoto T, Keiser MJ, Jacobson MP, Daneman R, Bainton RJ. Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior. Cell Rep. 2017 Oct 31; 21(5):1304-1316.
Boehm M, Beaumont K, Jones R, Kalgutkar AS, Zhang L, Atkinson K, Bai G, Brown JA, Eng H, Goetz GH, Holder BR, Khunte B, Lazzaro S, Limberakis C, Ryu S, Shapiro MJ, Tylaska L, Yan J, Turner R, Leung SSF, Ramaseshan M, Price DA, Liras S, Jacobson MP, Earp DJ, Lokey RS, Mathiowetz AM, Menhaji-Klotz E. Discovery of Potent and Orally Bioavailable Macrocyclic Peptide-Peptoid Hybrid CXCR7 Modulators. J Med Chem. 2017 12 14; 60(23):9653-9663.
White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal. 2017 Sep 05; 10(495).
Szpiech ZA, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez RD. Prominent features of the amino acid mutation landscape in cancer. PLoS One. 2017; 12(8):e0183273.
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. 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.
Tran HL, Lexa KW, Julien O, Young TS, Walsh CT, Jacobson MP, Wells JA. Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product. J Am Chem Soc. 2017 02 22; 139(7):2541-2544.
Metcalf B, Chuang C, Dufu K, Patel MP, Silva-Garcia A, Johnson C, Lu Q, Partridge JR, Patskovska L, Patskovsky Y, Almo SC, Jacobson MP, Hua L, Xu Q, Gwaltney SL, Yee C, Harris J, Morgan BP, James J, Xu D, Hutchaleelaha A, Paulvannan K, Oksenberg D, Li Z. Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin. ACS Med Chem Lett. 2017 Mar 09; 8(3):321-326.
Wang Q, Sciabola S, Barreiro G, Hou X, Bai G, Shapiro MJ, Koehn F, Villalobos A, Jacobson MP. Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction. J Chem Inf Model. 2016 11 28; 56(11):2194-2206.
He XY, Li YJ, Kalyanaraman C, Qiu LL, Chen C, Xiao Q, Liu WX, Zhang W, Yang JJ, Chen G, Jacobson MP, Shi YS. GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors. Proc Natl Acad Sci U S A. 2016 09 20; 113(38):E5645-54.
Armstrong M, van Hoorebeke C, Horn T, Deschamps J, Freedman JC, Kalyanaraman C, Jacobson MP, Holman T. Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency. Bioorg Med Chem. 2016 11 01; 24(21):5380-5387.
Tian B, Poulter CD, Jacobson MP. Defining the Product Chemical Space of Monoterpenoid Synthases. PLoS Comput Biol. 2016 08; 12(8):e1005053.
Coutsias EA, Lexa KW, Wester MJ, Pollock SN, Jacobson MP. Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics. J Chem Theory Comput. 2016 Sep 13; 12(9):4674-87.
de Jesus Cortez F, Suzawa M, Irvy S, Bruning JM, Sablin E, Jacobson MP, Fletterick RJ, Ingraham HA, England PM. Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2). PLoS One. 2016; 11(7):e0159316.
Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S, Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crécy-Lagard V, Jacobson MP, Almo SC, Gerlt JA. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc Natl Acad Sci U S A. 2016 07 19; 113(29):E4161-9.
Ball KA, Johnson JR, Lewinski MK, Guatelli J, Verschueren E, Krogan NJ, Jacobson MP. Non-degradative Ubiquitination of Protein Kinases. PLoS Comput Biol. 2016 06; 12(6):e1004898.
Leung SS, Sindhikara D, Jacobson MP. Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition. J Chem Inf Model. 2016 05 23; 56(5):924-9.
Armstrong MM, Freedman CJ, Jung JE, Zheng Y, Kalyanaraman C, Jacobson MP, Simeonov A, Maloney DJ, van Leyen K, Jadhav A, Holman TR. A potent and selective inhibitor targeting human and murine 12/15-LOX. Bioorg Med Chem. 2016 Mar 15; 24(6):1183-90.
Long T, Neitz RJ, Beasley R, Kalyanaraman C, Suzuki BM, Jacobson MP, Dissous C, McKerrow JH, Drewry DH, Zuercher WJ, Singh R, Caffrey CR. Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni. PLoS Negl Trop Dis. 2016 Jan; 10(1):e0004356.
Ahlbach CL, Lexa KW, Bockus AT, Chen V, Crews P, Jacobson MP, Lokey RS. Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products. Future Med Chem. 2015; 7(16):2121-30.
Schwochert J, Turner R, Thang M, Berkeley RF, Ponkey AR, Rodriguez KM, Leung SS, Khunte B, Goetz G, Limberakis C, Kalgutkar AS, Eng H, Shapiro MJ, Mathiowetz AM, Price DA, Liras S, Jacobson MP, Lokey RS. Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides. Org Lett. 2015 Jun 19; 17(12):2928-31.
Bockus AT, Lexa KW, Pye CR, Kalgutkar AS, Gardner JW, Hund KC, Hewitt WM, Schwochert JA, Glassey E, Price DA, Mathiowetz AM, Liras S, Jacobson MP, Lokey RS. Probing the Physicochemical Boundaries of Cell Permeability and Oral Bioavailability in Lipophilic Macrocycles Inspired by Natural Products. J Med Chem. 2015 Jun 11; 58(11):4581-9.
Chow JY, Tian BX, Ramamoorthy G, Hillerich BS, Seidel RD, Almo SC, Jacobson MP, Poulter CD. Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus. Proc Natl Acad Sci U S A. 2015 May 05; 112(18):5661-6.
Ramamoorthy G, Pugh ML, Tian BX, Phan RM, Perez LB, Jacobson MP, Poulter CD. Synthesis and enzymatic studies of bisubstrate analogues for farnesyl diphosphate synthase. J Org Chem. 2015 Apr 17; 80(8):3902-13.
Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJ. A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. J Biomol Screen. 2015 Jul; 20(6):788-800.
Zhang X, Kumar R, Vetting MW, Zhao S, Jacobson MP, Almo SC, Gerlt JA. A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily. J Am Chem Soc. 2015 Feb 04; 137(4):1388-91.
Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC. Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry. 2015 Jan 27; 54(3):909-31.
Hewitt WM, Leung SS, Pye CR, Ponkey AR, Bednarek M, Jacobson MP, Lokey RS. Cell-permeable cyclic peptides from synthetic libraries inspired by natural products. J Am Chem Soc. 2015 Jan 21; 137(2):715-21.
Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. PLoS Comput Biol. 2014 Oct; 10(10):e1003874.
Hasnain S, McClendon CL, Hsu MT, Jacobson MP, Bandyopadhyay P. A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion. PLoS One. 2014; 9(9):e106466.
Krishnan S, Miller RM, Tian B, Mullins RD, Jacobson MP, Taunton J. Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis. J Am Chem Soc. 2014 Sep 10; 136(36):12624-30.
Jameson JB, Kantz A, Schultz L, Kalyanaraman C, Jacobson MP, Maloney DJ, Jadhav A, Simeonov A, Holman TR. A high throughput screen identifies potent and selective inhibitors to human epithelial 15-lipoxygenase-2. PLoS One. 2014; 9(8):e104094.
Jacobson MP, Kalyanaraman C, Zhao S, Tian B. Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. Trends Biochem Sci. 2014 Aug; 39(8):363-71.
Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30; 3.
Groninger-Poe FP, Bouvier JT, Vetting MW, Kalyanaraman C, Kumar R, Almo SC, Jacobson MP, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58. Biochemistry. 2014 Jul 01; 53(25):4192-203.
Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model. 2014 Jun 23; 54(6):1687-99.
Lexa KW, Dolghih E, Jacobson MP. A structure-based model for predicting serum albumin binding. PLoS One. 2014; 9(4):e93323.
Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. mBio. 2014 Feb 11; 5(1):e00933-13.
Peng LX, Hsu MT, Bonomi M, Agard DA, Jacobson MP. The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery. PLoS Comput Biol. 2014 Feb; 10(2):e1003464.
Silber BM, Gever JR, Rao S, Li Z, Renslo AR, Widjaja K, Wong C, Giles K, Freyman Y, Elepano M, Irwin JJ, Jacobson MP, Prusiner SB. Novel compounds lowering the cellular isoform of the human prion protein in cultured human cells. Bioorg Med Chem. 2014 Mar 15; 22(6):1960-72.
Rardin MJ, He W, Nishida Y, Newman JC, Carrico C, Danielson SR, Guo A, Gut P, Sahu AK, Li B, Uppala R, Fitch M, Riiff T, Zhu L, Zhou J, Mulhern D, Stevens RD, Ilkayeva OR, Newgard CB, Jacobson MP, Hellerstein M, Goetzman ES, Gibson BW, Verdin E. SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. Cell Metab. 2013 Dec 03; 18(6):920-33.
Ndao M, Nath-Chowdhury M, Sajid M, Marcus V, Mashiyama ST, Sakanari J, Chow E, Mackey Z, Land KM, Jacobson MP, Kalyanaraman C, McKerrow JH, Arrowood MJ, Caffrey CR. A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection. Antimicrob Agents Chemother. 2013 Dec; 57(12):6063-73.
Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature. 2013 Oct 31; 502(7473):698-702.
Silber BM, Gever JR, Li Z, Gallardo-Godoy A, Renslo AR, Widjaja K, Irwin JJ, Rao S, Jacobson MP, Ghaemmaghami S, Prusiner SB. Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells. Bioorg Med Chem. 2013 Dec 15; 21(24):7999-8012.
Choi CH, Webb BA, Chimenti MS, Jacobson MP, Barber DL. pH sensing by FAK-His58 regulates focal adhesion remodeling. J Cell Biol. 2013 Sep 16; 202(6):849-59.
Lu D, Giles K, Li Z, Rao S, Dolghih E, Gever JR, Geva M, Elepano ML, Oehler A, Bryant C, Renslo AR, Jacobson MP, Dearmond SJ, Silber BM, Prusiner SB. Biaryl amides and hydrazones as therapeutics for prion disease in transgenic mice. J Pharmacol Exp Ther. 2013 Nov; 347(2):325-38.
Tian B, Wallrapp F, Kalyanaraman C, Zhao S, Eriksson LA, Jacobson MP. Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase. Biochemistry. 2013 Aug 20; 52(33):5511-3.
Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD. Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2. Structure. 2013 Sep 03; 21(9):1571-80.
Kim J, Xiao H, Bonanno JB, Kalyanaraman C, Brown S, Tang X, Al-Obaidi NF, Patskovsky Y, Babbitt PC, Jacobson MP, Lee YS, Almo SC. Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature. 2013 Jun 06; 498(7452):123-6.
Li Z, Silber BM, Rao S, Gever JR, Bryant C, Gallardo-Godoy A, Dolghih E, Widjaja K, Elepano M, Jacobson MP, Prusiner SB, Renslo AR. 2-Aminothiazoles with improved pharmacotherapeutic properties for treatment of prion disease. ChemMedChem. 2013 May; 8(5):847-57.
Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD. Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proc Natl Acad Sci U S A. 2013 Mar 26; 110(13):E1196-202.
Schönichen A, Webb BA, Jacobson MP, Barber DL. Considering protonation as a posttranslational modification regulating protein structure and function. Annu Rev Biophys. 2013; 42:289-314.
Silber BM, Rao S, Fife KL, Gallardo-Godoy A, Renslo AR, Dalvie DK, Giles K, Freyman Y, Elepano M, Gever JR, Li Z, Jacobson MP, Huang Y, Benet LZ, Prusiner SB. Pharmacokinetics and metabolism of 2-aminothiazoles with antiprion activity in mice. Pharm Res. 2013 Apr; 30(4):932-50.
Datta D, McClendon CL, Jacobson MP, Wells JA. Substrate and inhibitor-induced dimerization and cooperativity in caspase-1 but not caspase-3. J Biol Chem. 2013 Apr 05; 288(14):9971-9981.
Choy JW, Bryant C, Calvet CM, Doyle PS, Gunatilleke SS, Leung SS, Ang KK, Chen S, Gut J, Oses-Prieto JA, Johnston JB, Arkin MR, Burlingame AL, Taunton J, Jacobson MP, McKerrow JM, Podust LM, Renslo AR. Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein J Org Chem. 2013; 9:15-25.
Lokey RS, Liras J, Liras S, Jacobson MP. Designing molecules to cross biological membranes. Curr Top Med Chem. 2013; 13(7):775.
Spreafico M, Jacobson MP. In silico prediction of brain exposure: drug free fraction, unbound brain to plasma concentration ratio and equilibrium half-life. Curr Top Med Chem. 2013; 13(7):813-20.
Dolghih E, Jacobson MP. Predicting efflux ratios and blood-brain barrier penetration from chemical structure: combining passive permeability with active efflux by P-glycoprotein. ACS Chem Neurosci. 2013 Feb 20; 4(2):361-7.
Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJS, Jacobson MP, Kortemme T. Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. Structure. 2013 Jan 08; 21(1):54-64.
Rand AC, Leung SS, Eng H, Rotter CJ, Sharma R, Kalgutkar AS, Zhang Y, Varma MV, Farley KA, Khunte B, Limberakis C, Price DA, Liras S, Mathiowetz AM, Jacobson MP, Lokey RS. Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance(). Medchemcomm. 2012 Oct; 3(10):1282-1289.
Kuroda D, Shirai H, Jacobson MP, Nakamura H. Computer-aided antibody design. Protein Eng Des Sel. 2012 Oct; 25(10):507-21.
Leung SS, Mijalkovic J, Borrelli K, Jacobson MP. Testing physical models of passive membrane permeation. J Chem Inf Model. 2012 Jun 25; 52(6):1621-36.
McClendon CL, Hua L, Barreiro A, Jacobson MP. Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion. J Chem Theory Comput. 2012 Jul 12; 8(6):2115-2126.
Ingram JR, Rafi SB, Eroy-Reveles AA, Ray M, Lambeth L, Hsieh I, Ruelas D, Lim KC, Sakanari J, Craik CS, Jacobson MP, McKerrow JH. Investigation of the proteolytic functions of an expanded cercarial elastase gene family in Schistosoma mansoni. PLoS Negl Trop Dis. 2012; 6(4):e1589.
Kumar P, Chimenti MS, Pemble H, Schönichen A, Thompson O, Jacobson MP, Wittmann T. Multisite phosphorylation disrupts arginine-glutamate salt bridge networks required for binding of cytoplasmic linker-associated protein 2 (CLASP2) to end-binding protein 1 (EB1). J Biol Chem. 2012 May 18; 287(21):17050-17064.
Rafi SB, Hearn BR, Vedantham P, Jacobson MP, Renslo AR. Predicting and improving the membrane permeability of peptidic small molecules. J Med Chem. 2012 Apr 12; 55(7):3163-9.
Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci U S A. 2012 Mar 13; 109(11):4122-7.
Narayanan A, LeClaire LL, Barber DL, Jacobson MP. Phosphorylation of the Arp2 subunit relieves auto-inhibitory interactions for Arp2/3 complex activation. PLoS Comput Biol. 2011 Nov; 7(11):e1002226.
Gerlt JA, Babbitt PC, Jacobson MP, Almo SC. Divergent evolution in enolase superfamily: strategies for assigning functions. J Biol Chem. 2012 Jan 02; 287(1):29-34.
Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV. The Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62.
White TR, Renzelman CM, Rand AC, Rezai T, McEwen CM, Gelev VM, Turner RA, Linington RG, Leung SS, Kalgutkar AS, Bauman JN, Zhang Y, Liras S, Price DA, Mathiowetz AM, Jacobson MP, Lokey RS. On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds. Nat Chem Biol. 2011 Sep 25; 7(11):810-7.
MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA. Assessment of protein structure refinement in CASP9. Proteins. 2011; 79 Suppl 10:74-90.
Webb BA, Chimenti M, Jacobson MP, Barber DL. Dysregulated pH: a perfect storm for cancer progression. Nat Rev Cancer. 2011 08 11; 11(9):671-7.
Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP. A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series. J Chem Inf Model. 2011 Sep 26; 51(9):2082-9.
Dolghih E, Bryant C, Renslo AR, Jacobson MP. Predicting binding to p-glycoprotein by flexible receptor docking. PLoS Comput Biol. 2011 Jun; 7(6):e1002083.
Cossins BP, Jacobson MP, Guallar V. A new view of the bacterial cytosol environment. PLoS Comput Biol. 2011 Jun; 7(6):e1002066.
Nilmeier J, Hua L, Coutsias EA, Jacobson MP. Assessing protein loop flexibility by hierarchical Monte Carlo sampling. J Chem Theory Comput. 2011 May 10; 7(5):1564-1574.
Sadowsky JD, Burlingame MA, Wolan DW, McClendon CL, Jacobson MP, Wells JA. Turning a protein kinase on or off from a single allosteric site via disulfide trapping. Proc Natl Acad Sci U S A. 2011 Apr 12; 108(15):6056-61.
Wong SE, Sellers BD, Jacobson MP. Effects of somatic mutations on CDR loop flexibility during affinity maturation. Proteins. 2011 Mar; 79(3):821-9.
Morcos F, Chatterjee S, McClendon CL, Brenner PR, López-Rendón R, Zintsmaster J, Ercsey-Ravasz M, Sweet CR, Jacobson MP, Peng JW, Izaguirre JA. Modeling conformational ensembles of slow functional motions in Pin1-WW. PLoS Comput Biol. 2010 Dec 02; 6(12):e1001015.
Shimazu T, Hirschey MD, Hua L, Dittenhafer-Reed KE, Schwer B, Lombard DB, Li Y, Bunkenborg J, Alt FW, Denu JM, Jacobson MP, Verdin E. SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production. Cell Metab. 2010 Dec 01; 12(6):654-61.
Wong SE, Sellers BD, Jacobson MP. Effects of somatic mutations on CDR loop flexibility during affinity maturation. Proteins. 2010 Oct 19.
Sellers BD, Nilmeier JP, Jacobson MP. Antibodies as a model system for comparative model refinement. Proteins. 2010 Aug 15; 78(11):2490-505.
Wilbur JD, Hwang PK, Ybe JA, Lane M, Sellers BD, Jacobson MP, Fletterick RJ, Brodsky FM. Conformation switching of clathrin light chain regulates clathrin lattice assembly. Dev Cell. 2010 May 18; 18(5):841-8.
Kalyanaraman C, Jacobson MP. Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway. Biochemistry. 2010 May 18; 49(19):4003-5.
Doyle PS, Chen CK, Johnston JB, Hopkins SD, Leung SS, Jacobson MP, Engel JC, McKerrow JH, Podust LM. A nonazole CYP51 inhibitor cures Chagas' disease in a mouse model of acute infection. Antimicrob Agents Chemother. 2010 Jun; 54(6):2480-8.
Huang N, Jacobson MP. Binding-site assessment by virtual fragment screening. PLoS One. 2010 Apr 09; 5(4):e10109.
Chen CK, Leung SS, Guilbert C, Jacobson MP, McKerrow JH, Podust LM. Structural characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei bound to the antifungal drugs posaconazole and fluconazole. PLoS Negl Trop Dis. 2010 Apr 06; 4(4):e651.
Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis . Biochemistry. 2009 Dec 08; 48(48):11546-58.
Rapp CS, Schonbrun C, Jacobson MP, Kalyanaraman C, Huang N. Automated site preparation in physics-based rescoring of receptor ligand complexes. Proteins. 2009 Oct; 77(1):52-61.
McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP. Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. J Chem Theory Comput. 2009 Sep 08; 5(9):2486-2502.
Nilmeier J, Jacobson MP. Monte Carlo Sampling with Hierarchical Move Sets: POSH Monte Carlo. J Chem Theory Comput. 2009 Aug 11; 5(8):1968-84.
Farady CJ, Sellers BD, Jacobson MP, Craik CS. Improving the species cross-reactivity of an antibody using computational design. Bioorg Med Chem Lett. 2009 Jul 15; 19(14):3744-7.
Narayanan A, Jacobson MP. Computational studies of protein regulation by post-translational phosphorylation. Curr Opin Struct Biol. 2009 Apr; 19(2):156-63.
Narayanan A, Sellers BD, Jacobson MP. Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains. J Mol Biol. 2009 May 22; 388(5):941-53.
Tan ES, Naylor JC, Groban ES, Bunzow JR, Jacobson MP, Grandy DK, Scanlan TS. The molecular basis of species-specific ligand activation of trace amine-associated receptor 1 (TAAR(1)). ACS Chem Biol. 2009 Mar 20; 4(3):209-20.
Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009 Apr; 10(2):107-25.
Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9.
MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in CASP8. Proteins. 2009; 77 Suppl 9:66-80.
Frantz C, Barreiro G, Dominguez L, Chen X, Eddy R, Condeelis J, Kelly MJ, Jacobson MP, Barber DL. Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding. J Cell Biol. 2008 Dec 01; 183(5):865-79.
Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure. 2008 Nov 12; 16(11):1668-77.
Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 2008 Aug 15; 72(3):959-71.
Nilmeier J, Jacobson M. Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility. J Chem Theory Comput. 2008 May; 4(5):835-846.
Wong S, Jacobson MP. Conformational selection in silico: loop latching motions and ligand binding in enzymes. Proteins. 2008 Apr; 71(1):153-64.
Tan ES, Groban ES, Jacobson MP, Scanlan TS. Toward deciphering the code to aminergic G protein-coupled receptor drug design. Chem Biol. 2008 Apr; 15(4):343-53.
Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol. 2008 Mar 28; 377(3):914-34.
Kalyanaraman C, Jacobson MP. An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. J Comput Aided Mol Des. 2007 Dec; 21(12):675-9.
Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol. 2007 Aug; 3(8):486-91.
Huang N, Jacobson MP. Physics-based methods for studying protein-ligand interactions. Curr Opin Drug Discov Devel. 2007 May; 10(3):325-31.
Li X, Jacobson MP, Zhu K, Zhao S, Friesner RA. Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling. Proteins. 2007 Mar 01; 66(4):824-37.
Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes. J Chem Theory Comput. 2007 Mar; 3(2):640-8.
Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B. Prediction of side-chain conformations on protein surfaces. Proteins. 2007 Mar 01; 66(4):814-23.
Srivastava J, Barber DL, Jacobson MP. Intracellular pH sensors: design principles and functional significance. Physiology (Bethesda). 2007 Feb; 22:30-9.
Mandell DJ, Chorny I, Groban ES, Wong SE, Levine E, Rapp CS, Jacobson MP. Strengths of hydrogen bonds involving phosphorylated amino acid side chains. J Am Chem Soc. 2007 Jan 31; 129(4):820-7.
Rezai T, Bock JE, Zhou MV, Kalyanaraman C, Lokey RS, Jacobson MP. Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides. J Am Chem Soc. 2006 Nov 01; 128(43):14073-80.
Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys. 2006 Nov 28; 8(44):5166-77.
Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily. J Mol Biol. 2006 Jun 30; 360(1):228-50.
Groban ES, Narayanan A, Jacobson MP. Conformational changes in protein loops and helices induced by post-translational phosphorylation. PLoS Comput Biol. 2006 Apr; 2(4):e32.
Rezai T, Yu B, Millhauser GL, Jacobson MP, Lokey RS. Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers. J Am Chem Soc. 2006 Mar 01; 128(8):2510-1.
Kenyon V, Chorny I, Carvajal WJ, Holman TR, Jacobson MP. Novel human lipoxygenase inhibitors discovered using virtual screening with homology models. J Med Chem. 2006 Feb 23; 49(4):1356-63.
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem. 2006 Jan 26; 49(2):534-53.
Yu Z, Jacobson MP, Friesner RA. What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. J Comput Chem. 2006 Jan 15; 27(1):72-89.
Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. J Chem Inf Model. 2006 Jan-Feb; 46(1):243-53.
Chorny I, Dill KA, Jacobson MP. Surfaces affect ion pairing. J Phys Chem B. 2005 Dec 22; 109(50):24056-60.
Bernacki K, Kalyanaraman C, Jacobson MP. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods. J Biomol Screen. 2005 Oct; 10(7):675-81.
Wong SE, Bernacki K, Jacobson M. Competition between intramolecular hydrogen bonds and solvation in phosphorylated peptides: simulations with explicit and implicit solvent. J Phys Chem B. 2005 Mar 24; 109(11):5249-58.
Kalyanaraman C, Bernacki K, Jacobson MP. Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry. 2005 Feb 15; 44(6):2059-71.
Ruddat VC, Mogul R, Chorny I, Chen C, Perrin N, Whitman S, Kenyon V, Jacobson MP, Bernasconi CF, Holman TR. Tryptophan 500 and arginine 707 define product and substrate active site binding in soybean lipoxygenase-1. Biochemistry. 2004 Oct 19; 43(41):13063-71.
Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins. 2004 May 01; 55(2):351-67.
Li X, Jacobson MP, Friesner RA. High-resolution prediction of protein helix positions and orientations. Proteins. 2004 May 01; 55(2):368-82.
Guallar V, Jacobson M, McDermott A, Friesner RA. Computational modeling of the catalytic reaction in triosephosphate isomerase. J Mol Biol. 2004 Mar 12; 337(1):227-39.
Coutsias EA, Seok C, Jacobson MP, Dill KA. A kinematic view of loop closure. J Comput Chem. 2004 Mar; 25(4):510-28.
Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol. 2002 Jul 12; 320(3):597-608.
Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. J Struct Funct Genomics. 2002; 2(2):103-11.
Silva ML, Jacobson MP, Duan Z, and Field RW. Journal of Chemical Physics. Unexpected Simplicity in the S1 -> S0 Dispersed Fluorescence Spectrum of 13C2H2. 2002; 16:7939–7947.