Matt Jacobson, PhD
Professor Emeritus
Pharmaceutical Chemistry
School of Pharmacy

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

Awards

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• UCSF School of Pharmacy Dean’s Recognition for Excellence in Teaching, 2006
• Alfred P. Sloan Research Fellowship, 2004
• NSF CAREER Award, 2004
• National Science Foundation Postdoctoral Fellowship in Biological Informatics, 2000-2002
• Air Force Research Laboratory, Space Vehicles Directorate “Team Publication of the Year Award”, 2000
• EPSRC (Engineering and Physical Sciences Research Council, U.K.) Visiting Fellow, 1999-2000
• Fannie and John Hertz Fellow, 1998-1999
• Rao Prize, for “outstanding student talk” at the International Symposium on Molecular Spectroscopy, Ohio State University, 1997
• National Defense Science and Engineering Graduate Fellow, 1995-1998
• American Institute of Chemists Graduation Award, Stanford University, 1993
• Phi Beta Kappa, Stanford University, 1993
• David Starr Jordan Scholar, Stanford University, 1989

Education & Training

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• Post-doctoral Chemistry Columbia 2002
• Post-doctoral Physical Chemistry Oxford 2000
• Ph.D. Physical Chemistry MIT 1999
• B.S. Chemistry Stanford 1993

Websites

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• Profile at jacobson.compbio.ucsf.edu (jacobsonlab.org)

Grants and Projects

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• Molecular Biophysics Training Grant, NIH, 1988-2023
• HARC Center: HIV Accessory and Regulatory Complexes, NIH, 2007-2022
• Novel Strategies for the Discovery of Microbial Metabolic Pathways, NIH, 2016-2021
• Collaborative Center for an Enzyme Function Initiative, NIH, 2010-2016
• Understanding, Predicting, and Engineering Membrane Permeability, NIH, 2009-2014
• Resource for Biocomputing, Visualization, and Informatics, NIH/NCRR, 1976-2012
• Physics-Based Refinement of Comparative Protein Models, NIH, 2007-2011

Publications (183)

Top publication keywords:
Lipoxygenase InhibitorsComputational BiologyPiebaldismMolecular Docking SimulationEnzymesComputer SimulationProtein ConformationArachidonate 12-LipoxygenaseMolecular Dynamics SimulationModels, MolecularPhosphopyruvate HydrataseProteinsAlkyl and Aryl TransferasesArachidonate 15-LipoxygenaseCell Membrane Permeability

• Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Chow JY, Tian BX, Ramamoorthy G, Hillerich BS, Seidel RD, Almo SC, Jacobson MP, Poulter CD
• Discovery of new enzymes and metabolic pathways by using structure and genome context.
  Nature 2013 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
• Testing physical models of passive membrane permeation.
  Journal of chemical information and modeling 2012 Leung SS, Mijalkovic J, Borrelli K, Jacobson MP
• On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds.
  Nature chemical biology 2011 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
• Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles.
  Journal of chemical theory and computation 2009 McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP
• Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides.
  Journal of the American Chemical Society 2006 Rezai T, Bock JE, Zhou MV, Kalyanaraman C, Lokey RS, Jacobson MP
• A hierarchical approach to all-atom protein loop prediction.
  Proteins 2004 Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA

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• BCR::ABL1 kinase N-lobe mutants confer moderate to high degrees of resistance to asciminib.
  Blood 2024 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
• Identifying FUS amyotrophic lateral sclerosis disease signatures in patient dermal fibroblasts.
  Developmental cell 2024 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
• A role for pH dynamics regulating transcription factor DNA binding selectivity.
  bioRxiv : the preprint server for biology 2024 Kisor KP, Ruiz DG, Jacobson MP, Barber DL
• Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2023 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…
• Searching for molecular hypoxia sensors among oxygen-dependent enzymes.
  eLife 2023 Li L, Shen S, Bickler P, Jacobson MP, Wu LF, Altschuler SJ
• Correction: Mutations in α-synuclein, TDP-43 and tau prolong protein half-life through diminished degradation by lysosomal proteases.
  Molecular neurodegeneration 2023 Sampognaro PJ, Arya S, Knudsen GM, Gunderson EL, Sandoval-Perez A, Hodul M, Bowles K, Craik CS, Jacobson MP, Kao AW
• Signal peptide mimicry primes Sec61 for client-selective inhibition.
  Nature chemical biology 2023 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, …
• Dissecting the effects of GTPase and kinase domain mutations on LRRK2 endosomal localization and activity.
  Cell reports 2023 Rinaldi C, Waters CS, Li Z, Kumbier K, Rao L, Nichols RJ, Jacobson MP, Wu LF, Altschuler SJ
• Mutations in α-synuclein, TDP-43 and tau prolong protein half-life through diminished degradation by lysosomal proteases.
  Molecular neurodegeneration 2023 Sampognaro PJ, Arya S, Knudsen GM, Gunderson EL, Sandoval-Perez A, Hodul M, Bowles K, Craik CS, Jacobson MP, Kao AW
• Correction to "Assessing the Activation of Tyrosine Kinase KIT through Free Energy Calculations".
  Journal of chemical theory and computation 2022 Sandoval-Pérez A, Winger BA, Jacobson MP
• Fighting Plasmodium chloroquine resistance with acetylenic chloroquine analogues.
  International journal for parasitology. Drugs and drug resistance 2022 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, …
• Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor.
  Science (New York, N.Y.) 2022 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, …
• Assessing the Activation of Tyrosine Kinase KIT through Free Energy Calculations.
  Journal of chemical theory and computation 2022 Sandoval-Pérez A, Winger BA, Jacobson MP
• Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation.
  Biochemistry 2022 Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP
• Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters.
  Science advances 2022 Sun X, Bieber JM, Hammerlindl H, Chalkley RJ, Li KH, Burlingame AL, Jacobson MP, Wu LF, Altschuler SJ
• Kinetic and structural investigations of novel inhibitors of human epithelial 15-lipoxygenase-2.
  Bioorganic & medicinal chemistry 2021 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, …
• Docking and mutagenesis studies lead to improved inhibitor development of ML355 for human platelet 12-lipoxygenase.
  Bioorganic & medicinal chemistry 2021 Tsai WC, Aleem AM, Tena J, Rivera-Velazquez M, Brah HS, Tripathi S, D'silva M, Nadler JL, Kalyanaraman C, Jacobson MP, Holman T
• Analogs of the Dopamine Metabolite 5,6-Dihydroxyindole Bind Directly to and Activate the Nuclear Receptor Nurr1.
  ACS chemical biology 2021 Kholodar SA, Lang G, Cortopassi WA, Iizuka Y, Brah HS, Jacobson MP, England PM
• 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 Tsai WC, Kalyanaraman C, Yamaguchi A, Holinstat M, Jacobson MP, Holman TR
• Protomer alignment modulates specificity of RNA substrate recognition by Ire1.
  eLife 2021 Li W, Crotty K, Garrido Ruiz D, Voorhies M, Rivera C, Sil A, Mullins RD, Jacobson MP, Peschek J, Walter P
• Gasdermin D pore structure reveals preferential release of mature interleukin-1.
  Nature 2021 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
• A Crowding Barrier to Protein Inhibition in Colloidal Aggregates.
  Journal of medicinal chemistry 2021 Lak P, O'Donnell H, Du X, Jacobson MP, Shoichet BK
• Mutagenesis, Hydrogen-Deuterium Exchange, and Molecular Docking Investigations Establish the Dimeric Interface of Human Platelet-Type 12-Lipoxygenase.
  Biochemistry 2021 Tsai WC, Aleem AM, Whittington C, Cortopassi WA, Kalyanaraman C, Baroz A, Iavarone AT, Skrzypczak-Jankun E, Jacobson MP, Offenbacher AR, Holman T
• Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium.
  Cancer discovery 2021 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 …
• Synthesis and Screening of α-Xylosides in Human Glioblastoma Cells.
  Molecular pharmaceutics 2020 Kalita M, Villanueva-Meyer J, Ohkawa Y, Kalyanaraman C, Chen K, Mohamed E, Parker MFL, Jacobson MP, Phillips JJ, Evans MJ, Wilson DM
• 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 Perry SC, Horn T, Tourdot BE, Yamaguchi A, Kalyanaraman C, Conrad WS, Akinkugbe O, Holinstat M, Jacobson MP, Holman TR
• Synthetic group A streptogramin antibiotics that overcome Vat resistance.
  Nature 2020 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…
• The Synthesis and Structural Requirements for Measuring Glucocorticoid Receptor Expression In Vivo with (±)-11C-YJH08 PET.
  Journal of nuclear medicine : official publication, Society of Nuclear Medicine 2020 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
• 15-Lipoxygenase-1 biosynthesis of 7S,14S-diHDHA implicates 15-lipoxygenase-2 in biosynthesis of resolvin D5.
  Journal of lipid research 2020 Perry SC, Kalyanaraman C, Tourdot BE, Conrad WS, Akinkugbe O, Freedman JC, 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 Freedman C, Tran A, Tourdot BE, Kalyanaraman C, Perry S, Holinstat M, Jacobson MP, Holman TR
• A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
  Nature 2020 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, …
• A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.
  bioRxiv : the preprint server for biology 2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, …
• Age- and stress-associated C. elegans granulins impair lysosomal function and induce a compensatory HLH-30/TFEB transcriptional response.
  PLoS genetics 2019 Butler VJ, Gao F, Corrales CI, Cortopassi WA, Caballero B, Vohra M, Ashrafi K, Cuervo AM, Jacobson MP, Coppola G, Kao AW
• ATP-Competitive Inhibitors Midostaurin and Avapritinib Have Distinct Resistance Profiles in Exon 17-Mutant KIT.
  Cancer research 2019 Apsel Winger B, Cortopassi WA, Garrido Ruiz D, Ding L, Jang K, Leyte-Vidal A, Zhang N, Esteve-Puig R, Jacobson MP, Shah NP
• Multi-Granulin Domain Peptides Bind to Pro-Cathepsin D and Stimulate Its Enzymatic Activity More Effectively Than Progranulin in Vitro.
  Biochemistry 2019 Butler VJ, Cortopassi WA, Gururaj S, Wang AL, Pierce OM, Jacobson MP, Kao AW
• Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins.
  Molecular cell 2019 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
• Tau repeat regions contain conserved histidine residues that modulate microtubule-binding in response to changes in pH.
  The Journal of biological chemistry 2019 Charafeddine RA, Cortopassi WA, Lak P, Tan R, McKenney RJ, Jacobson MP, Barber DL, Wittmann T
• Conformational Dynamics of the HIV-Vif Protein Complex.
  Biophysical journal 2019 Ball KA, Chan LM, Stanley DJ, Tierney E, Thapa S, Ta HM, Burton L, Binning JM, Jacobson MP, Gross JD
• Structure-based identification of novel CK2 inhibitors with a linear 2-propenone scaffold as anti-cancer agents.
  Biochemical and biophysical research communications 2019 Qi X, Zhang N, Zhao L, Hu L, Cortopassi WA, Jacobson MP, Li X, Zhong R
• Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite.
  Cell chemical biology 2019 Bruning JM, Wang Y, Oltrabella F, Tian B, Kholodar SA, Liu H, Bhattacharya P, Guo S, Holton JM, Fletterick RJ, Jacobson MP, England PM
• Progranulin Stimulates the In Vitro Maturation of Pro-Cathepsin D at Acidic pH.
  Journal of molecular biology 2019 Butler VJ, Cortopassi WA, Argouarch AR, Ivry SL, Craik CS, Jacobson MP, Kao AW
• Probing the Electrostatic and Steric Requirements for Substrate Binding in Human Platelet-Type 12-Lipoxygenase.
  Biochemistry 2019 Aleem AM, Tsai WC, Tena J, Alvarez G, Deschamps J, Kalyanaraman C, Jacobson MP, Holman T
• Inhibitor binding mode and allosteric regulation of Na+-glucose symporters.
  Nature communications 2018 Bisignano P, Ghezzi C, Jo H, Polizzi NF, Althoff T, Kalyanaraman C, Friemann R, Jacobson MP, Wright EM, Grabe M
• Structure-based Discovery of Novel CK2α-Binding Cyclic Peptides with Anti-cancer Activity.
  Molecular informatics 2018 Tang S, Zhang N, Zhou Y, Cortopassi WA, Jacobson MP, Zhao LJ, Zhong RG
• Exploration of Benzothiazole Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70).
  Journal of medicinal chemistry 2018 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
• A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle.
  Nature communications 2018 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…
• High-throughput screen for inhibitors of protein-protein interactions in a reconstituted heat shock protein 70 (Hsp70) complex.
  The Journal of biological chemistry 2018 Taylor IR, Dunyak BM, Komiyama T, Shao H, Ran X, Assimon VA, Kalyanaraman C, Rauch JN, Jacobson MP, Zuiderweg ERP, Gestwicki JE
• Prediction of enzymatic pathways by integrative pathway mapping.
  eLife 2018 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, …
• Development of 5N-Bicalutamide, a High-Affinity Reversible Covalent Antiandrogen.
  ACS chemical biology 2017 de Jesus Cortez F, Nguyen P, Truillet C, Tian B, Kuchenbecker KM, Evans MJ, Webb P, Jacobson MP, Fletterick RJ, England PM
• Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior.
  Cell reports 2017 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
• Discovery of Potent and Orally Bioavailable Macrocyclic Peptide-Peptoid Hybrid CXCR7 Modulators.
  Journal of medicinal chemistry 2017 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 …
• Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins.
  Science signaling 2017 White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL
• Prominent features of the amino acid mutation landscape in cancer.
  PloS one 2017 Szpiech ZA, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez RD
• Synthesis of the Ca2+-mobilizing messengers NAADP and cADPR by intracellular CD38 enzyme in the mouse heart: Role in β-adrenoceptor signaling.
  The Journal of biological chemistry 2017 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
• Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product.
  Journal of the American Chemical Society 2017 Tran HL, Lexa KW, Julien O, Young TS, Walsh CT, Jacobson MP, Wells JA
• Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin.
  ACS medicinal chemistry letters 2017 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, …
• Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction.
  Journal of chemical information and modeling 2016 Wang Q, Sciabola S, Barreiro G, Hou X, Bai G, Shapiro MJ, Koehn F, Villalobos A, Jacobson MP
• GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors.
  Proceedings of the National Academy of Sciences of the United States of America 2016 He XY, Li YJ, Kalyanaraman C, Qiu LL, Chen C, Xiao Q, Liu WX, Zhang W, Yang JJ, Chen G, Jacobson MP, Shi YS
• Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency.
  Bioorganic & medicinal chemistry 2016 Armstrong M, van Hoorebeke C, Horn T, Deschamps J, Freedman JC, Kalyanaraman C, Jacobson MP, Holman T
• Defining the Product Chemical Space of Monoterpenoid Synthases.
  PLoS computational biology 2016 Tian B, Poulter CD, Jacobson MP
• Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics.
  Journal of chemical theory and computation 2016 Coutsias EA, Lexa KW, Wester MJ, Pollock SN, Jacobson MP
• Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2).
  PloS one 2016 de Jesus Cortez F, Suzawa M, Irvy S, Bruning JM, Sablin E, Jacobson MP, Fletterick RJ, Ingraham HA, England PM
• Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars.
  Proceedings of the National Academy of Sciences of the United States of America 2016 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
• Non-degradative Ubiquitination of Protein Kinases.
  PLoS computational biology 2016 Ball KA, Johnson JR, Lewinski MK, Guatelli J, Verschueren E, Krogan NJ, Jacobson MP
• Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition.
  Journal of chemical information and modeling 2016 Leung SS, Sindhikara D, Jacobson MP
• A potent and selective inhibitor targeting human and murine 12/15-LOX.
  Bioorganic & medicinal chemistry 2016 Armstrong MM, Freedman CJ, Jung JE, Zheng Y, Kalyanaraman C, Jacobson MP, Simeonov A, Maloney DJ, van Leyen K, Jadhav A, Holman TR
• Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni.
  PLoS neglected tropical diseases 2016 Long T, Neitz RJ, Beasley R, Kalyanaraman C, Suzuki BM, Jacobson MP, Dissous C, McKerrow JH, Drewry DH, Zuercher WJ, Singh R, Caffrey CR
• Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products.
  Future medicinal chemistry 2015 Ahlbach CL, Lexa KW, Bockus AT, Chen V, Crews P, Jacobson MP, Lokey RS
• Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides.
  Organic letters 2015 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 …
• Probing the Physicochemical Boundaries of Cell Permeability and Oral Bioavailability in Lipophilic Macrocycles Inspired by Natural Products.
  Journal of medicinal chemistry 2015 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
• Synthesis and enzymatic studies of bisubstrate analogues for farnesyl diphosphate synthase.
  The Journal of organic chemistry 2015 Ramamoorthy G, Pugh ML, Tian BX, Phan RM, Perez LB, Jacobson MP, Poulter CD
• A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP.
  Journal of biomolecular screening 2015 Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJ
• A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily.
  Journal of the American Chemical Society 2015 Zhang X, Kumar R, Vetting MW, Zhao S, Jacobson MP, Almo SC, Gerlt JA
• Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
  Biochemistry 2015 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, …
• Cell-permeable cyclic peptides from synthetic libraries inspired by natural products.
  Journal of the American Chemical Society 2015 Hewitt WM, Leung SS, Pye CR, Ponkey AR, Bednarek M, Jacobson MP, Lokey RS
• Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach.
  PLoS computational biology 2014 Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP
• 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 Hasnain S, McClendon CL, Hsu MT, Jacobson MP, Bandyopadhyay P
• Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis.
  Journal of the American Chemical Society 2014 Krishnan S, Miller RM, Tian B, Mullins RD, Jacobson MP, Taunton J
• A high throughput screen identifies potent and selective inhibitors to human epithelial 15-lipoxygenase-2.
  PloS one 2014 Jameson JB, Kantz A, Schultz L, Kalyanaraman C, Jacobson MP, Maloney DJ, Jadhav A, Simeonov A, Holman TR
• Leveraging structure for enzyme function prediction: methods, opportunities, and challenges.
  Trends in biochemical sciences 2014 Jacobson MP, Kalyanaraman C, Zhao S, Tian B
• Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.
  eLife 2014 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
• Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58.
  Biochemistry 2014 Groninger-Poe FP, Bouvier JT, Vetting MW, Kalyanaraman C, Kumar R, Almo SC, Jacobson MP, Gerlt JA
• Prediction of substrates for glutathione transferases by covalent docking.
  Journal of chemical information and modeling 2014 Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A
• A structure-based model for predicting serum albumin binding.
  PloS one 2014 Lexa KW, Dolghih E, Jacobson MP
• Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.
  mBio 2014 Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE
• The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery.
  PLoS computational biology 2014 Peng LX, Hsu MT, Bonomi M, Agard DA, Jacobson MP
• Novel compounds lowering the cellular isoform of the human prion protein in cultured human cells.
  Bioorganic & medicinal chemistry 2014 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
• SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks.
  Cell metabolism 2013 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, …
• A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection.
  Antimicrobial agents and chemotherapy 2013 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
• Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells.
  Bioorganic & medicinal chemistry 2013 Silber BM, Gever JR, Li Z, Gallardo-Godoy A, Renslo AR, Widjaja K, Irwin JJ, Rao S, Jacobson MP, Ghaemmaghami S, Prusiner SB
• pH sensing by FAK-His58 regulates focal adhesion remodeling.
  The Journal of cell biology 2013 Choi CH, Webb BA, Chimenti MS, Jacobson MP, Barber DL
• Biaryl amides and hydrazones as therapeutics for prion disease in transgenic mice.
  The Journal of pharmacology and experimental therapeutics 2013 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
• Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase.
  Biochemistry 2013 Tian B, Wallrapp F, Kalyanaraman C, Zhao S, Eriksson LA, Jacobson MP
• Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2.
  Structure (London, England : 1993) 2013 Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD
• Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function.
  Nature 2013 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
• 2-Aminothiazoles with improved pharmacotherapeutic properties for treatment of prion disease.
  ChemMedChem 2013 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
• Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD
• Considering protonation as a posttranslational modification regulating protein structure and function.
  Annual review of biophysics 2013 Schönichen A, Webb BA, Jacobson MP, Barber DL
• Pharmacokinetics and metabolism of 2-aminothiazoles with antiprion activity in mice.
  Pharmaceutical research 2013 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
• Substrate and inhibitor-induced dimerization and cooperativity in caspase-1 but not caspase-3.
  The Journal of biological chemistry 2013 Datta D, McClendon CL, Jacobson MP, Wells JA
• Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target.
  Beilstein journal of organic chemistry 2013 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
• Designing molecules to cross biological membranes.
  Current topics in medicinal chemistry 2013 Lokey RS, Liras J, Liras S, Jacobson MP
• In silico prediction of brain exposure: drug free fraction, unbound brain to plasma concentration ratio and equilibrium half-life.
  Current topics in medicinal chemistry 2013 Spreafico M, Jacobson MP
• Predicting efflux ratios and blood-brain barrier penetration from chemical structure: combining passive permeability with active efflux by P-glycoprotein.
  ACS chemical neuroscience 2012 Dolghih E, Jacobson MP
• Design of a phosphorylatable PDZ domain with peptide-specific affinity changes.
  Structure (London, England : 1993) 2012 Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJS, Jacobson MP, Kortemme T
• Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance().
  MedChemComm 2012 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
• Computer-aided antibody design.
  Protein engineering, design & selection : PEDS 2012 Kuroda D, Shirai H, Jacobson MP, Nakamura H
• Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion.
  Journal of chemical theory and computation 2012 McClendon CL, Hua L, Barreiro A, Jacobson MP
• Investigation of the proteolytic functions of an expanded cercarial elastase gene family in Schistosoma mansoni.
  PLoS neglected tropical diseases 2012 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
• Multisite phosphorylation disrupts arginine-glutamate salt bridge networks required for binding of cytoplasmic linker-associated protein 2 (CLASP2) to end-binding protein 1 (EB1).
  The Journal of biological chemistry 2012 Kumar P, Chimenti MS, Pemble H, Schönichen A, Thompson O, Jacobson MP, Wittmann T
• Predicting and improving the membrane permeability of peptidic small molecules.
  Journal of medicinal chemistry 2012 Rafi SB, Hearn BR, Vedantham P, Jacobson MP, Renslo AR
• Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
  Proceedings of the National Academy of Sciences of the United States of America 2012 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
• Phosphorylation of the Arp2 subunit relieves auto-inhibitory interactions for Arp2/3 complex activation.
  PLoS computational biology 2011 Narayanan A, LeClaire LL, Barber DL, Jacobson MP
• Divergent evolution in enolase superfamily: strategies for assigning functions.
  The Journal of biological chemistry 2011 Gerlt JA, Babbitt PC, Jacobson MP, Almo SC
• The Enzyme Function Initiative.
  Biochemistry 2011 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
• Assessment of protein structure refinement in CASP9.
  Proteins 2011 MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA
• Dysregulated pH: a perfect storm for cancer progression.
  Nature reviews. Cancer 2011 Webb BA, Chimenti M, Jacobson MP, Barber DL
• A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series.
  Journal of chemical information and modeling 2011 Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP
• Predicting binding to p-glycoprotein by flexible receptor docking.
  PLoS computational biology 2011 Dolghih E, Bryant C, Renslo AR, Jacobson MP
• A new view of the bacterial cytosol environment.
  PLoS computational biology 2011 Cossins BP, Jacobson MP, Guallar V
• Assessing protein loop flexibility by hierarchical Monte Carlo sampling.
  Journal of chemical theory and computation 2011 Nilmeier J, Hua L, Coutsias EA, Jacobson MP
• Turning a protein kinase on or off from a single allosteric site via disulfide trapping.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Sadowsky JD, Burlingame MA, Wolan DW, McClendon CL, Jacobson MP, Wells JA
• Effects of somatic mutations on CDR loop flexibility during affinity maturation.
  Proteins 2010 Wong SE, Sellers BD, Jacobson MP
• Modeling conformational ensembles of slow functional motions in Pin1-WW.
  PLoS computational biology 2010 Morcos F, Chatterjee S, McClendon CL, Brenner PR, López-Rendón R, Zintsmaster J, Ercsey-Ravasz M, Sweet CR, Jacobson MP, Peng JW, Izaguirre JA
• SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production.
  Cell metabolism 2010 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
• Effects of somatic mutations on CDR loop flexibility during affinity maturation.
  Proteins 2010 Wong SE, Sellers BD, Jacobson MP
• Antibodies as a model system for comparative model refinement.
  Proteins 2010 Sellers BD, Nilmeier JP, Jacobson MP
• Conformation switching of clathrin light chain regulates clathrin lattice assembly.
  Developmental cell 2010 Wilbur JD, Hwang PK, Ybe JA, Lane M, Sellers BD, Jacobson MP, Fletterick RJ, Brodsky FM
• Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway.
  Biochemistry 2010 Kalyanaraman C, Jacobson MP
• A nonazole CYP51 inhibitor cures Chagas' disease in a mouse model of acute infection.
  Antimicrobial agents and chemotherapy 2010 Doyle PS, Chen CK, Johnston JB, Hopkins SD, Leung SS, Jacobson MP, Engel JC, McKerrow JH, Podust LM
• Binding-site assessment by virtual fragment screening.
  PloS one 2010 Huang N, Jacobson MP
• Structural characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei bound to the antifungal drugs posaconazole and fluconazole.
  PLoS neglected tropical diseases 2010 Chen CK, Leung SS, Guilbert C, Jacobson MP, McKerrow JH, Podust LM
• Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis .
  Biochemistry 2009 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
• Automated site preparation in physics-based rescoring of receptor ligand complexes.
  Proteins 2009 Rapp CS, Schonbrun C, Jacobson MP, Kalyanaraman C, Huang N
• Monte Carlo Sampling with Hierarchical Move Sets: POSH Monte Carlo.
  Journal of chemical theory and computation 2009 Nilmeier J, Jacobson MP
• Improving the species cross-reactivity of an antibody using computational design.
  Bioorganic & medicinal chemistry letters 2009 Farady CJ, Sellers BD, Jacobson MP, Craik CS
• Computational studies of protein regulation by post-translational phosphorylation.
  Current opinion in structural biology 2009 Narayanan A, Jacobson MP
• Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains.
  Journal of molecular biology 2009 Narayanan A, Sellers BD, Jacobson MP
• The molecular basis of species-specific ligand activation of trace amine-associated receptor 1 (TAAR(1)).
  ACS chemical biology 2009 Tan ES, Naylor JC, Groban ES, Bunzow JR, Jacobson MP, Grandy DK, Scanlan TS
• Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
  Journal of structural and functional genomics 2009 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, …
• Outcome of a workshop on applications of protein models in biomedical research.
  Structure (London, England : 1993) 2009 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…
• Assessment of the protein-structure refinement category in CASP8.
  Proteins 2009 MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA
• Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding.
  The Journal of cell biology 2008 Frantz C, Barreiro G, Dominguez L, Chen X, Eddy R, Condeelis J, Kelly MJ, Jacobson MP, Barber DL
• Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
  Structure (London, England : 1993) 2008 Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP
• Toward better refinement of comparative models: predicting loops in inexact environments.
  Proteins 2008 Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP
• Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility.
  Journal of chemical theory and computation 2008 Nilmeier J, Jacobson M
• Conformational selection in silico: loop latching motions and ligand binding in enzymes.
  Proteins 2008 Wong S, Jacobson MP
• Toward deciphering the code to aminergic G protein-coupled receptor drug design.
  Chemistry & biology 2008 Tan ES, Groban ES, Jacobson MP, Scanlan TS
• Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
  Journal of molecular biology 2008 Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK
• An atomistic model of passive membrane permeability: application to a series of FDA approved drugs.
  Journal of computer-aided molecular design 2007 Kalyanaraman C, Jacobson MP
• Prediction and assignment of function for a divergent N-succinyl amino acid racemase.
  Nature chemical biology 2007 Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA
• Physics-based methods for studying protein-ligand interactions.
  Current opinion in drug discovery & development 2007 Huang N, Jacobson MP
• 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 Li X, Jacobson MP, Zhu K, Zhao S, Friesner RA
• Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes.
  Journal of chemical theory and computation 2007 Zhu K, Shirts MR, Friesner RA, Jacobson MP
• Prediction of side-chain conformations on protein surfaces.
  Proteins 2007 Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B
• Intracellular pH sensors: design principles and functional significance.
  Physiology (Bethesda, Md.) 2007 Srivastava J, Barber DL, Jacobson MP
• Strengths of hydrogen bonds involving phosphorylated amino acid side chains.
  Journal of the American Chemical Society 2007 Mandell DJ, Chorny I, Groban ES, Wong SE, Levine E, Rapp CS, Jacobson MP
• Molecular mechanics methods for predicting protein-ligand binding.
  Physical chemistry chemical physics : PCCP 2006 Huang N, Kalyanaraman C, Bernacki K, Jacobson MP
• Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily.
  Journal of molecular biology 2006 Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC
• Conformational changes in protein loops and helices induced by post-translational phosphorylation.
  PLoS computational biology 2006 Groban ES, Narayanan A, Jacobson MP
• Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers.
  Journal of the American Chemical Society 2006 Rezai T, Yu B, Millhauser GL, Jacobson MP, Lokey RS
• Novel human lipoxygenase inhibitors discovered using virtual screening with homology models.
  Journal of medicinal chemistry 2006 Kenyon V, Chorny I, Carvajal WJ, Holman TR, Jacobson MP
• Novel procedure for modeling ligand/receptor induced fit effects.
  Journal of medicinal chemistry 2006 Sherman W, Day T, Jacobson MP, Friesner RA, Farid R
• What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules.
  Journal of computational chemistry 2006 Yu Z, Jacobson MP, Friesner RA
• Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening.
  Journal of chemical information and modeling 2006 Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP
• Surfaces affect ion pairing.
  The journal of physical chemistry. B 2005 Chorny I, Dill KA, Jacobson MP
• Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods.
  Journal of biomolecular screening 2005 Bernacki K, Kalyanaraman C, Jacobson MP
• Competition between intramolecular hydrogen bonds and solvation in phosphorylated peptides: simulations with explicit and implicit solvent.
  The journal of physical chemistry. B 2005 Wong SE, Bernacki K, Jacobson M
• Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes.
  Biochemistry 2005 Kalyanaraman C, Bernacki K, Jacobson MP
• Tryptophan 500 and arginine 707 define product and substrate active site binding in soybean lipoxygenase-1.
  Biochemistry 2004 Ruddat VC, Mogul R, Chorny I, Chen C, Perrin N, Whitman S, Kenyon V, Jacobson MP, Bernasconi CF, Holman TR
• High-resolution prediction of protein helix positions and orientations.
  Proteins 2004 Li X, Jacobson MP, Friesner RA
• Computational modeling of the catalytic reaction in triosephosphate isomerase.
  Journal of molecular biology 2004 Guallar V, Jacobson M, McDermott A, Friesner RA
• A kinematic view of loop closure.
  Journal of computational chemistry 2004 Coutsias EA, Seok C, Jacobson MP, Dill KA
• On the role of the crystal environment in determining protein side-chain conformations.
  Journal of molecular biology 2002 Jacobson MP, Friesner RA, Xiang Z, Honig B
• Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction.
  Journal of structural and functional genomics 2002 Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM
• Journal of Chemical Physics
  Unexpected Simplicity in the S1 -> S0 Dispersed Fluorescence Spectrum of 13C2H2 2002 Silva ML, Jacobson MP, Duan Z, and Field RW