Matthew P Jacobson

Matthew P Jacobson

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Matthew P Jacobson

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Multi-Granulin Domain Peptides Bind to Pro-Cathepsin D and Stimulate Its Enzymatic Activity More Effectively Than Progranulin in Vitro.

Biochemistry 2019 Jun 24;58(23):2670-2674. Epub 2019 May 24.

Department of Neurology , University of California , San Francisco , California 94143 , United States.

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http://dx.doi.org/10.1021/acs.biochem.9b00275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6666309PMC
June 2019

Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite.

Cell Chem Biol 2019 May 7;26(5):674-685.e6. Epub 2019 Mar 7.

Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2019.02.002DOI Listing
May 2019

Tau repeat regions contain conserved histidine residues that modulate microtubule-binding in response to changes in pH.

J Biol Chem 2019 May 16;294(22):8779-8790. Epub 2019 Apr 16.

From the Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California 94143,

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http://dx.doi.org/10.1074/jbc.RA118.007004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6552421PMC
May 2019

Structure-based identification of novel CK2 inhibitors with a linear 2-propenone scaffold as anti-cancer agents.

Biochem Biophys Res Commun 2019 Apr 14;512(2):208-212. Epub 2019 Mar 14.

Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China.

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http://dx.doi.org/10.1016/j.bbrc.2019.03.016DOI Listing
April 2019

Conformational Dynamics of the HIV-Vif Protein Complex.

Biophys J 2019 Apr 23;116(8):1432-1445. Epub 2019 Mar 23.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2019.03.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486493PMC
April 2019

Structure-based Discovery of Novel CK2α-Binding Cyclic Peptides with Anti-cancer Activity.

Mol Inform 2019 03 11;38(3):e1800089. Epub 2018 Oct 11.

Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China.

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http://dx.doi.org/10.1002/minf.201800089DOI Listing
March 2019

Progranulin Stimulates the In Vitro Maturation of Pro-Cathepsin D at Acidic pH.

J Mol Biol 2019 Mar 25;431(5):1038-1047. Epub 2019 Jan 25.

Department of Neurology, University of California, San Francisco, CA 94143, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.01.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6613950PMC
March 2019

Probing the Electrostatic and Steric Requirements for Substrate Binding in Human Platelet-Type 12-Lipoxygenase.

Biochemistry 2019 02 4;58(6):848-857. Epub 2019 Jan 4.

Department of Chemistry and Biochemistry , University of California Santa Cruz , Santa Cruz , California 95064 , United States.

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http://dx.doi.org/10.1021/acs.biochem.8b01167DOI Listing
February 2019

Exploration of Benzothiazole Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70).

J Med Chem 2018 Jul 13;61(14):6163-6177. Epub 2018 Jul 13.

Department of Pharmaceutical Chemistry , University of California at San Francisco , Sandler Center, 675 Nelson Rising Lane , San Francisco , California 94158 , United States.

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http://dx.doi.org/10.1021/acs.jmedchem.8b00583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104643PMC
July 2018

Development of 5N-Bicalutamide, a High-Affinity Reversible Covalent Antiandrogen.

ACS Chem Biol 2017 12 2;12(12):2934-2939. Epub 2017 Nov 2.

Department of Pharmaceutical Chemistry, University of California San Francisco , 600 16th Street, San Francisco, California 94158, United States.

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http://dx.doi.org/10.1021/acschembio.7b00702DOI Listing
December 2017

Prominent features of the amino acid mutation landscape in cancer.

PLoS One 2017 24;12(8):e0183273. Epub 2017 Aug 24.

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183273PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570307PMC
October 2017

Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins.

Sci Signal 2017 Sep 5;10(495). Epub 2017 Sep 5.

Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1126/scisignal.aam9931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022362PMC
September 2017

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 13;139(7):2541-2544. Epub 2017 Feb 13.

Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jacs.6b10792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345905PMC
February 2017

Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency.

Bioorg Med Chem 2016 11 31;24(21):5380-5387. Epub 2016 Aug 31.

Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065787PMC
http://dx.doi.org/10.1016/j.bmc.2016.08.063DOI Listing
November 2016

Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction.

J Chem Inf Model 2016 11 21;56(11):2194-2206. Epub 2016 Oct 21.

Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States.

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http://dx.doi.org/10.1021/acs.jcim.6b00237DOI Listing
November 2016

Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics.

J Chem Theory Comput 2016 Sep 4;12(9):4674-87. Epub 2016 Aug 4.

Department of Pharmaceutical Chemistry, University of California in San Francisco , San Francisco, California 94107, United States.

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http://dx.doi.org/10.1021/acs.jctc.6b00250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465426PMC
September 2016

GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors.

Proc Natl Acad Sci U S A 2016 09 6;113(38):E5645-54. Epub 2016 Sep 6.

State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061 China;

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5035880PMC
http://dx.doi.org/10.1073/pnas.1524358113DOI Listing
September 2016

Defining the Product Chemical Space of Monoterpenoid Synthases.

PLoS Comput Biol 2016 08 12;12(8):e1005053. Epub 2016 Aug 12.

Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982680PMC
August 2016

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 11;113(29):E4161-9. Epub 2016 Jul 11.

Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801

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http://dx.doi.org/10.1073/pnas.1605546113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961189PMC
July 2016

Non-degradative Ubiquitination of Protein Kinases.

PLoS Comput Biol 2016 06 2;12(6):e1004898. Epub 2016 Jun 2.

Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890936PMC
June 2016

Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition.

J Chem Inf Model 2016 05 2;56(5):924-9. Epub 2016 May 2.

Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States.

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http://dx.doi.org/10.1021/acs.jcim.6b00005DOI Listing
May 2016

A potent and selective inhibitor targeting human and murine 12/15-LOX.

Bioorg Med Chem 2016 Mar 21;24(6):1183-90. Epub 2016 Jan 21.

Chemistry and Biochemistry Department, University of California, Santa Cruz, CA 95060, United States. Electronic address:

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http://dx.doi.org/10.1016/j.bmc.2016.01.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778748PMC
March 2016

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 11;10(1):e0004356. Epub 2016 Jan 11.

Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, California, United States of America.

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http://dx.doi.org/10.1371/journal.pntd.0004356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709140PMC
January 2016

A structure-based model for predicting serum albumin binding.

PLoS One 2014 1;9(4):e93323. Epub 2014 Apr 1.

Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093323PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3972100PMC
December 2015

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 17;20(6):788-800. Epub 2015 Feb 17.

Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA

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http://dx.doi.org/10.1177/1087057115570550DOI Listing
July 2015

Probing the Physicochemical Boundaries of Cell Permeability and Oral Bioavailability in Lipophilic Macrocycles Inspired by Natural Products.

J Med Chem 2015 Jun 20;58(11):4581-9. Epub 2015 May 20.

†Department of Chemistry and Biochemistry, University of California-Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States.

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http://dx.doi.org/10.1021/acs.jmedchem.5b00128DOI Listing
June 2015

Synthesis and enzymatic studies of bisubstrate analogues for farnesyl diphosphate synthase.

J Org Chem 2015 Apr 26;80(8):3902-13. Epub 2015 Mar 26.

†Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States.

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http://dx.doi.org/10.1021/acs.joc.5b00202DOI Listing
April 2015

A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily.

J Am Chem Soc 2015 Feb 26;137(4):1388-91. Epub 2015 Jan 26.

Departments of Biochemistry and Chemistry and ‡Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

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http://dx.doi.org/10.1021/ja5103986DOI Listing
February 2015

Cell-permeable cyclic peptides from synthetic libraries inspired by natural products.

J Am Chem Soc 2015 Jan 8;137(2):715-21. Epub 2015 Jan 8.

Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States.

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http://dx.doi.org/10.1021/ja508766bDOI Listing
January 2015

Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach.

PLoS Comput Biol 2014 Oct 9;10(10):e1003874. Epub 2014 Oct 9.

Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1003874
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http://dx.doi.org/10.1371/journal.pcbi.1003874DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191879PMC
October 2014

Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis.

J Am Chem Soc 2014 Sep 2;136(36):12624-30. Epub 2014 Sep 2.

Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California-San Francisco , San Francisco, California 94158, United States.

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http://dx.doi.org/10.1021/ja505194wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160273PMC
September 2014

Leveraging structure for enzyme function prediction: methods, opportunities, and challenges.

Trends Biochem Sci 2014 Aug 2;39(8):363-71. Epub 2014 Jul 2.

Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA.

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http://www.cell.com/trends/biochemical-sciences/pdf/S0968-00
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http://linkinghub.elsevier.com/retrieve/pii/S096800041400091
Publisher Site
http://dx.doi.org/10.1016/j.tibs.2014.05.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117707PMC
August 2014

Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58.

Biochemistry 2014 Jul 19;53(25):4192-203. Epub 2014 Jun 19.

Department of Biochemistry, ‡Department of Chemistry, and §Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.

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http://dx.doi.org/10.1021/bi5005377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081050PMC
July 2014

Prediction of substrates for glutathione transferases by covalent docking.

J Chem Inf Model 2014 Jun 16;54(6):1687-99. Epub 2014 May 16.

Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco , San Francisco, California 94158, United States.

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http://dx.doi.org/10.1021/ci5001554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4068255PMC
June 2014

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

Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005893PMC
http://dx.doi.org/10.2174/1568026611313070004DOI Listing
April 2014

Novel compounds lowering the cellular isoform of the human prion protein in cultured human cells.

Bioorg Med Chem 2014 Mar 9;22(6):1960-72. Epub 2014 Jan 9.

Institute for Neurodegenerative Diseases, University of California, San Francisco, United States; Department of Neurology, University of California, San Francisco, United States. Electronic address:

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http://dx.doi.org/10.1016/j.bmc.2014.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984052PMC
March 2014

The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery.

PLoS Comput Biol 2014 Feb 6;10(2):e1003464. Epub 2014 Feb 6.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America ; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1003464
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http://dx.doi.org/10.1371/journal.pcbi.1003464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916224PMC
February 2014

A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection.

Antimicrob Agents Chemother 2013 Dec 23;57(12):6063-73. Epub 2013 Sep 23.

National Reference Centre for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada.

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http://dx.doi.org/10.1128/AAC.00734-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837922PMC
December 2013

Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells.

Bioorg Med Chem 2013 Dec 18;21(24):7999-8012. Epub 2013 Sep 18.

Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143, United States; Department of Neurology, University of California, San Francisco, CA 94143, United States; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, United States.

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https://linkinghub.elsevier.com/retrieve/pii/S09680896130080
Publisher Site
http://dx.doi.org/10.1016/j.bmc.2013.09.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984054PMC
December 2013

Biaryl amides and hydrazones as therapeutics for prion disease in transgenic mice.

J Pharmacol Exp Ther 2013 Nov 21;347(2):325-38. Epub 2013 Aug 21.

Institute for Neurodegenerative Diseases (D.L., K.G., Z.L., S.R., J.R.G., M.G., M.L.E., S.J.D., B.M.S., S.B.P.), Department of Neurology (K.G., Z.L., S.R., J.R.G., B.M.S., S.B.P.), Department of Pathology (A.O., S.J.D.), Department of Pharmaceutical Chemistry (E.D., C.B., A.R.R., M.P.J.), Department of Bioengineering and Therapeutic Sciences (B.M.S.), and Small Molecule Discovery Center (C.B., A.R.R.), University of California, San Francisco, California.

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http://dx.doi.org/10.1124/jpet.113.205799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807058PMC
November 2013

Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2.

Structure 2013 Sep 1;21(9):1571-80. Epub 2013 Aug 1.

Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1016/j.str.2013.06.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769517PMC
September 2013

pH sensing by FAK-His58 regulates focal adhesion remodeling.

J Cell Biol 2013 Sep;202(6):849-59

Department of Cell and Tissue Biology and 2 Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143.

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http://dx.doi.org/10.1083/jcb.201302131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3776353PMC
September 2013

Considering protonation as a posttranslational modification regulating protein structure and function.

Annu Rev Biophys 2013 28;42:289-314. Epub 2013 Feb 28.

Department of Cell and Tissue Biology, University of California, San Francisco, USA.

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http://dx.doi.org/10.1146/annurev-biophys-050511-102349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041481PMC
July 2013

Substrate and inhibitor-induced dimerization and cooperativity in caspase-1 but not caspase-3.

J Biol Chem 2013 Apr 5;288(14):9971-81. Epub 2013 Feb 5.

Department of Pharmaceutical Chemistry, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1074/jbc.M112.426460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617296PMC
April 2013

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.

Proc Natl Acad Sci U S A 2013 Mar 14;110(13):E1196-202. Epub 2013 Mar 14.

Department of Pharmaceutical Chemistry, School of Pharmacy and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1073/pnas.1300632110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612614PMC
March 2013

Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target.

Beilstein J Org Chem 2013 4;9:15-25. Epub 2013 Jan 4.

Small Molecule Discovery Center, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA ; Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA ; Department of Cellular and Molecular Pharmacology, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA.

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http://dx.doi.org/10.3762/bjoc.9.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566858PMC
February 2013

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 11;4(2):361-7. Epub 2012 Dec 11.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1021/cn3001922DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582291PMC
February 2013

Design of a phosphorylatable PDZ domain with peptide-specific affinity changes.

Structure 2013 Jan 15;21(1):54-64. Epub 2012 Nov 15.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4(th) Street, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, 1700 4(th) Street, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2012.10.007DOI Listing
January 2013

Computer-aided antibody design.

Protein Eng Des Sel 2012 Oct 2;25(10):507-21. Epub 2012 Jun 2.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, Japan.

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http://dx.doi.org/10.1093/protein/gzs024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3449398PMC
October 2012

Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion.

J Chem Theory Comput 2012 Jul 13;8(6):2115-2126. Epub 2012 Apr 13.

Graduate Group in Biophysics, University of California San Francisco.

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http://dx.doi.org/10.1021/ct300008dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538811PMC
July 2012

Testing physical models of passive membrane permeation.

J Chem Inf Model 2012 Jun 24;52(6):1621-36. Epub 2012 May 24.

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA.

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http://pubs.acs.org/doi/10.1021/ci200583t
Publisher Site
http://dx.doi.org/10.1021/ci200583tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383340PMC
June 2012

Predicting and improving the membrane permeability of peptidic small molecules.

J Med Chem 2012 Apr 20;55(7):3163-9. Epub 2012 Mar 20.

Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA.

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http://dx.doi.org/10.1021/jm201634qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325374PMC
April 2012

Divergent evolution in enolase superfamily: strategies for assigning functions.

J Biol Chem 2012 Jan 8;287(1):29-34. Epub 2011 Nov 8.

Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA.

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http://dx.doi.org/10.1074/jbc.R111.240945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249080PMC
January 2012

Assessment of protein structure refinement in CASP9.

Proteins 2011 30;79 Suppl 10:74-90. Epub 2011 Aug 30.

Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.

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http://dx.doi.org/10.1002/prot.23131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3238793PMC
December 2011

Phosphorylation of the Arp2 subunit relieves auto-inhibitory interactions for Arp2/3 complex activation.

PLoS Comput Biol 2011 Nov 10;7(11):e1002226. Epub 2011 Nov 10.

Graduate Group in Biophysics, University of California, San Francisco, San Francisco, California, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220268PMC
November 2011

A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series.

J Chem Inf Model 2011 Sep 9;51(9):2082-9. Epub 2011 Aug 9.

Department of Chemistry, Stern College for Women, Yeshiva University, New York, New York, United States.

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http://dx.doi.org/10.1021/ci200033nDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183355PMC
September 2011

Dysregulated pH: a perfect storm for cancer progression.

Nat Rev Cancer 2011 08 11;11(9):671-7. Epub 2011 Aug 11.

Department of Cell and Tissue Biology, University of California, San Francisco, California 94143, USA.

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http://dx.doi.org/10.1038/nrc3110DOI Listing
August 2011

A new view of the bacterial cytosol environment.

PLoS Comput Biol 2011 Jun 9;7(6):e1002066. Epub 2011 Jun 9.

Department of Life Science, Barcelona Supercomputer Center, Barcelona, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111478PMC
June 2011

Predicting binding to p-glycoprotein by flexible receptor docking.

PLoS Comput Biol 2011 Jun 23;7(6):e1002083. Epub 2011 Jun 23.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121697PMC
June 2011

Assessing protein loop flexibility by hierarchical Monte Carlo sampling.

J Chem Theory Comput 2011 May;7(5):1564-1574

Department of Pharmaceutical Chemistry, University of California in San Francisco, San Francisco, California 94158-2517.

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http://dx.doi.org/10.1021/ct1006696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129859PMC
May 2011

Turning a protein kinase on or off from a single allosteric site via disulfide trapping.

Proc Natl Acad Sci U S A 2011 Apr 23;108(15):6056-61. Epub 2011 Mar 23.

Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, 1700 Fourth Street, San Francisco, CA 94158, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076885PMC
April 2011

Effects of somatic mutations on CDR loop flexibility during affinity maturation.

Proteins 2011 Mar 6;79(3):821-9. Epub 2010 Dec 6.

Graduate Group in Biophysics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA.

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March 2011

Antibodies as a model system for comparative model refinement.

Proteins 2010 Aug;78(11):2490-505

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA.

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http://dx.doi.org/10.1002/prot.22757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998178PMC
August 2010

Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway.

Biochemistry 2010 May;49(19):4003-5

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA.

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http://dx.doi.org/10.1021/bi100445gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877507PMC
May 2010

Binding-site assessment by virtual fragment screening.

PLoS One 2010 Apr 9;5(4):e10109. Epub 2010 Apr 9.

National Institute of Biological Sciences, Beijing, Beijing, China.

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April 2010