M. Armstrong, C. van Hoorebeke, T. Horn, J. Deschamps, J. C. Freedman, C. Kalyanaraman, M. P. Jacobson, and T. Holman. “Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency”, Bioorg. Med. Chem., 24 (2016) 5380-5387. PMC5065787
Tag Archives: Docking
147.
F. de Jesus Cortez, M. Suzawa, S. Irvy, J. M. Bruning, E. Sablin, M. P. Jacobson, R. J. Fletterick, H. A. Ingraham, and P. M. England. “Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2)”, PLoS One, 11 (2016) e0159316. PMC4965143
146.
M. M. Armstrong, C. J. Freedman, J. E. Jung, Y. Zheng, C. Kalyanaraman, M. P. Jacobson, A. Simeonov, D. J. Maloney, K. van Leyen, A. Jadhav, and T. R. Holman. “A potent and selective inhibitor targeting human and murine 12/15-LOX”, Bioorg. Med. Chem., 24 (2016) 1183-1190. PMC4778748
145.
X. Zhang, M. S. Carter, M. W. Vetting, B. San Francisco, S. Zhao, N. F. Al-Obaidi, J. O. Solbiati, J. J. Thiaville, V. de Crécy-Lagard, M. P. Jacobson, S. C. Almo, and J. A. Gerlt. “Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars”, PNAS, 113 (2016) E4161-4169. PMC4961189
142.
T. Long, R. J. Neitz, R. Beasley, C. Kalyanaraman, B. M. Suzuki, M. P. Jacobson, C. Dissous, J. H. McKerrow, D. H. Drewry, W. J. Zuercher, R. Singh, and C. R. Caffrey. “Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni”, PLoS Negl. Trop. Dis., 10 (2016) e0004356. Open Access
138.
J.-Y. Chow, B.-X. Tian, G. Ramamoorthy, B. S. Hillerich, R. D. Seidel, S. C. Almo, M. P. Jacobson, and C. D. Poulter. “Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus”, PNAS 112 (2015) 5661-5666. PMC4426440
137.
G. Ramamoorthy, M. L. Pugh, B.-X. Tian, R. M. Phan, L. B. Perez, M. P. Jacobson, and C. D. Poulter. “Synthesis and Enzymatic Studies of Bisubstrate Analogues for Farnesyl Diphosphate Synthase”, Journal of Organic Chemistry, 80 (2015) 3902-3913. Pubmed
132.
B. Tian, F. H. Wallrapp, G. L. Holiday, J.-Y.Chow, P. C. Babbitt, C. D. Poulter, and M. P. Jacobson. “Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-Intermediate Docking Approach”, PLoS Computational Biology, 10 (2014) e1003874. PMC25299649
128.
J. B. Jameson, A. Kantz, L. Schultz, C. Kalyanaraman, M. P. Jacobson, D. J. Maloney, A. Jadhav, A. Simeonov, and T. R. Holman. “A high throughput screen identifies potent and selective inhibitors to human epithelial 15-lipoxygenase-2”. PLoS One, 9 (2014) e104094. PMC4128814
126.
F. P. Groninger-Poe, J. T. Bouvier, M. W. Vetting, C. Kalyanaraman, R. Kumar, S. C. Almo, M. P. Jacobson, and J. A. Gerlt. “Evolution of Enzymatic Activities in the Enolase Superfamily: Galactarate Dehydratase-III from Agrobacterium tumefaciens C58”, Biochemistry 53 (2014) 4192-4203. Online PMC4081050
124.
G. Q. Dong, S. Calhoun, H. Fan, C. Kalyanaraman, M. Branch, S. Mashiyama, N. London, M. P. Jacobson, P. C. Babbitt, R. Armstrong, A. Sali. “Prediction of substrates for glutathione transferases by covalent docking”, Journal of Chemical Information and Modeling, 54 (2014) 232-235. Online PMC4068255
123.
K. Lexa, E. Dolghih, A. Wiser, and M. P. Jacobson. “A Structure-Based Model for Predicting Serum Albumin Binding”, PLoS ONE, 9 (2014) e93323. PMC3972100
122.
R. Kumar, S. Zhao, M. W. Vetting, B. M. Wood, A. Sakai, K. Cho, S. C. Almo, J. V. Sweedler, M. P. Jacobson, J. A. Gerlt, and J. E. Cronan. “Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine”, mBio, 11 (2014) e00933-13. PMC3950512
117.
M. Ndao, M. Nath-Chowdhury, M. Sajid, V. Marcus, S. T. Mashiyama, J. Sakanari, E. Chow, Z. Mackey, K. M. Land, M. P. Jacobson, C. Kalyanaraman, J. H. McKerrow, M. J. Arrowood, C. R. Caffrey. “A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection”, Antimicrobial Agents and Chemotherapy, 57 (2013) 6063-6073. Online PMC3837922
114.
S. Zhao, R. Kumar, A. Sakai, M. Vetting, B. M. Wood, S. Brown, P. C. Babbitt, S. C. Almo, J. V. Sweedler, J. A. Gerlt, J. E. Cronan, and M. P. Jacobson. “Discovery of new enzymes and metabolic pathways using structure and genome context”, Nature, 502 (2013) 698-702. Online F1000 [News&Views: M. J. Wargo, “Digging up enzyme functions“, Nature Chemical Biology (2013).] [Discussed in PSI/Nature Knowledgbase] PMC3966649
110.
J. Kim, H. Xiao, X. Tang, C. Kalyanaraman, Y. Patskovsky, P. C. Babbitt, M. P. Jacobson, Y.-S. Lee and S. C. Almo. “PDB to Pathway: structure-guided discovery of carboxy-SAM as a novel metabolite for tRNA wobble base modification”, Nature, 498 (2013) 123-126. Online News&Views PMC23676670
107.
F. H. Wallrapp, J.-J. Pan, G. Ramamoorthy, D. E. Almonacid, B. S. Hillerich, R. Seidel, Y. Patskovsky, P. C. Babbitt, S. C. Almo, M. P. Jacobson and C. D. Poulter. “Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily”. PNAS, 110 (2013) E1196-E1202. Open access PMC3612614
106.
Z. Li, B. M. Silber, S. Rao, J. Gever, C. Bryant, A. Gallardo-Godoy, E. Dolghih, K. Widjaja, M. Elepano, M. P. Jacobson, S. B. Prusiner and A. R. Renslo. “2-Aminothiazoles with Improved Pharmacotherapeutic Properties for Treatment of Prion Disease”, ChemMedChem, 8 (2013) 847-857. PMC3984044
105.
J. W. Choy, C. Bryant, C. M. Calvet, P. S. Doyle, S. S. Gunatilleke, S. S. F. Leung, K. K. H. Ang, S. Chen, J. Gut, J. A. Oses-Prieto, J. B. Johnston, M. R. Arkin, A. L. Burlingame, J. Taunton, M. P. Jacobson, J. M. McKerrow, L. M. Podust, and A. R. Renslo. “Chemical-Biological Characterization of a Cruzain Inhibitor Reveals a Second Target and a Mammalian Off-Target”. Beilstein J. Org. Chem, 9 (2013) 15-25. PMC3566858
93.
T. Lukk, A. Sakai, C. Kalyanaraman, S. Brown, H. J. Imker, L. Song, A. A. Fedorov, E. V. Fedorov, R. Toro, B. Hillerich, R. Seidel, Y. Patskovsky, M. W. Vetting, S. K. Nair, P. C. Babbitt, S. C. Almo, J. A. Gerlt, and M. P. Jacobson. “Computational prediction of the diversity of enzyme specificity among dipeptide epimerases in the enolase superfamily”. PNAS, 109 (2012) 4122-4127. [F1000] [Discussion in PSI/Nature Knowledgebase] [Chemical&Engineering News] PMC3306705
88.
C. S. Rapp, C. Kalyanaraman, A. Schiffmiller, E. L. Schoenbrun, and M. P. Jacobson. “A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series”, Journal of Chemical Information and Modeling, 51 (2011) 2082-2089. PMC3183355
85.
E. Dolghih, C. Bryant, A. R. Renslo, and M. P. Jacobson. “Predicting binding to P-glycoprotein by flexible receptor docking”, PLoS Computational Biology, 7 (2011) e1002083. PMC3121697
82.
J. D. Sadowsky, M. A. Burlingame, D. W. Wolan, C. L. McClendon, M. P. Jacobson and J. A. Wells. “Turning a protein kinase (PDK1) on or off from a single allosteric site via disulfide trapping”. PNAS, 108 (2011) 6056-6061. PMC21430264
78.
C. Kalyanaraman and M. P. Jacobson. “Studying enzyme-substrate specificity in silico: A case study of the E. coli glycolysis pathway” (Rapid Report), Biochemistry, 49 (2010) 4003-4005. PMC2877507
77.
P. S. Doyle, C.-K. Chen, J. B. Johnston, S. Hopkins, S. S. F. Leung, M. P. Jacobson, J. C. Engel, J. H. McKerrow, L. M. Podust. “A Non-azole CYP51 Inhibitor Cures Chagas Disease in a Mouse Model of Acute Infection”, Antimicrobial Agents and Chemotherapy, 54 (2010) 2480-2488. PMC2876414
76.
N. Huang and M. P. Jacobson. “Virtual Fragment Screening for Binding Site Assessment”, PLoS One, 5 (2010) e10109. PMC2852417
73.
C.-K. Chen, S. S. F. Leung, C. Guilbert, M. P. Jacobson, J. H. McKerrow, and L. M. Podust. “Structural characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei bound to the antifungal drugs posaconazole and fluconazole”. PLoS Neglected Tropical Diseases, 4 (2010) e651. PMC2850312
70.
J. F. Rakus, C. Kalyanaraman, A. A. Fedorov, Elena V. Fedorov, F. P. Mills-Groninger, K. Bain, J. M. Sauder, S. K. Burley, S. C. Almo, M. P. Jacobson, and J. A. Gerlt. “Computation Facilitated Assignment of Function in the Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase from Oceanobacillus iheyensis”, Biochemistry, 48 (2009) 11546-58. PMC2787699
67.
E. S. Tan, J. C. Naylor, E. S. Groban, J. R. Bunzow, M. P. Jacobson, D. K. Grandy, and T. S. Scanlan. “The Molecular Basis of Species-Specific Ligand Activation of Trace Amine-Associated Receptor 1 (TAAR1)”, ACS Chemical Biology, 20 (2009) 209–220. PMC2677188
63.
C. S. Rapp, C. Schonbrun, M. P. Jacobson and Niu Huang. “Automated Site Preparation in Rescoring of Receptor Ligand Complexes”, Proteins, 77 (2009) 52-61. PMC2744578
60.
C. Kalyanaraman, H. J. Imker, A. A. Federov, E. V. Federov, M. E. Glasner, P. C. Babbitt, S. C. Almo, J. A. Gerlt, and M. P. Jacobson. “Discovery of a new dipeptide epimerase enzymatic function guided by homology modeling and virtual screening”, Structure, 16 (2008) 1668–1677. [Preview: D. Dunaway-Mariano, “Enzyme Function Discovery“, 16 (2008) 1599–1600.] Online PMC2714228
58.
E. S. Tan, E. S. Groban, M. P. Jacobson, and T. S. Scanlan. “Deciphering the Code to Aminergic G-Protein Coupled Receptor Drug Design.” Chemistry and Biology, 15 (2008) 343–353. Online PMC2713717
56.
A. P. Graves, D. M. Shivakumar, S. E. Boyce, M. P. Jacobson, D. A. Case, and B. K. Shoichet. “Rescoring docking hit lists for model cavity sites: predictions and experimental testing”, Journal of Molecular Biology, 377 (2008) 914–934. Online PMC2752715
55.
S. Wong and M. P. Jacobson. “In Silico Conformational Selection: Ligand-Induced Loop Latching”, Proteins, 71 (2008) 153–164. Online
52.
L. Song, C. Kalyanaraman, A. A. Fedorov, E. V. Fedorov, M. E. Glasner, S. Brown, P. C. Babbitt, S. C. Almo, M. P. Jacobson, and J. A. Gerlt. “Assignment and Prediction of Function in the Enolase Superfamily: A Divergent N-Succinyl Amino Acid Racemase from Bacillus cereus“, Nature Chemical Biology, 3 (2007) 486–491. [News&Views: K. N. Allen, “Form finds function“, Nature Chemical Biology, 3 (2007) 452–453.] [NIGMS “Biomedical Beat“] F1000 Online
51.
N. Huang and M. P. Jacobson. “New Physics-Based Methods for Studying Protein-Ligand Interactions”, Current Opinion in Drug Discovery & Development, 10 (2007) 325-331.
45.
N. Huang, C. Kalyanaraman, K. Bernacki, and M. P. Jacobson. “Molecular Mechanics Methods for Predicting Protein-Ligand Binding” (invited feature article), Physical Chemistry Chemical Physics, 8 (2006) 5166–5177. [PCCP “hot paper”; top downloaded papers in 2006.] Online
40.
V. Kenyon, I. Chorny, T. R. Holman, and M. P. Jacobson. “Novel human lipoxygenase inhibitors discovered using virtual screening with homology models”, Journal of Medicinal Chemistry, 49 (2006) 1356–1363. Online
39.
W. Sherman, T. Day, M. P. Jacobson, R. A. Friesner, and R. Farid. “Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects”, Journal of Medicinal Chemistry, 49 (2006) 534–553. [#3 most cited article in J Med Chem in 2006] Online
38.
N. Huang, C. Kalyanaraman, J. J. Irwin, and M. P. Jacobson. “Physics-Based Scoring of Protein-Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening”, Journal of Chemical Information and Modeling, 46 (2006) 243–253. Online
35.
K. Bernacki, C. Kalyanaraman, and M. P. Jacobson. “Virtual ligand Screening against E. coli Dihydrofolate Reductase: Improving Docking Enrichment Using Physics-Based Methods” (invited paper), Journal of Biomolecular Screening, 10 (2005) 675–681. Online
The Jacobson Laboratory at UCSF 