B. X. Tian, C. D. Poulter, and M. P. Jacobson. “Defining the Product Chemical Space of Monoterpenoid Synthases”, PLoS Computational Biology, 12 (2016) e1005053. PMC4982680
Category Archives: Enzyme Function Prediction
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
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
136.
X. Zhang, R. Kumar, M. W. Vetting, S. Zhao, M. P. Jacobson, S. C. Almo, and J. A. Gerlt. “A Novel Cis-3-Hydroxy-L-proline Dehydratase in the Enolase Superfamily”, JACS, 137 (2015) 1388-1391. Pubmed
135.
M. W. Vetting, N. Al-Obadi, S. Zhao, B. San Francisco, J. Kin, D. W. Wichelecki, J. Bouvier, J. O. Solbiati, H. Vu, X. Zhang, D. Rodionov, J. D. Love, B. S. Hillerich, R. D. Seidel, R. J. Quinn, A. L. Osterman, J. E. Cronan, M. P. Jacobson, J. A. Gerlt, S. C. Almo. “Experimental Strategies for Functional Annotation and Metabolism Discovery: Targeted Screening of Solute Binding Proteins and Unbiased Panning of Metabolomes”. Biochemistry, 54 (2015) 909-931. PMC4310620 C&ENews
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
127.
M. P. Jacobson, C. Kalyanaraman, S. Zhao, and B. Tian. “Leveraging structure for enzyme function prediction: methods, opportunities and challenges”, Trends in Biochemical Sciences 39 (2014), 363-371. Online PMC4117707
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
125.
S. Zhao, A. Sakai, X. Zhang, M. Vetting, R. Kumar, B. Hillerich, B. San Francisco, J. Solbiati, A. Steeves, S. Brown, E. Akiva, A. Barber, R. Seidel, J. E. Cronan, P. C. Babbitt, S. C. Almo, J. A. Gerlt, and M. P. Jacobson. “Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks”, eLife (2014) e03275. Online PMC4113996
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
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
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
113.
B. Tian, F. Wallrapp, C. Kalyanaraman, S. Zhao, L. A. Eriksson, and M. P. Jacobson. “Predicting Enzyme-Substrate Specificity with QM/MM Methods: A Case Study of the Stereo-specificity of D-glucarate Dehydratase”. Biochemistry, 52 (2013) 5511-5513. Online PMC3964877
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
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
92.
J. A. Gerlt, P. C. Babbitt, M. P. Jacobson, and S. C. Almo. “Divergent evolution in the enolase superfamily: Strategies for assigning functions” (mini-review). Journal of Biological Chemistry, 287 (2012) 29-34. PMC3249080
90.
J. A. Gerlt, K. N. Allen, S. C. Almo, R. N. Armstrong, P. C. Babbitt, J. E. Cronan, D. Dunaway-Mariano, H. J. Imker, M. P. Jacobson, W. Minor, C. D. Poulter, F. M. Raushel, A. Sali, B. K. Shoichet, and J. V. Sweedler. “The Enzyme Function Initiative”, Biochemistry, 50 (2011) 9950-9962. PMC3238057
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
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
62.
U. Pieper, R. Chiang, J. J. Seffernick, S. D. Brown, M. E. Glasner, L. Kelly, N. Eswar, M. Sauder, S. K. Burley, S. Almo, J. A. Gerlt, F. Raushel, B. K. Shoichet, M. P. Jacobson, P. C. Babbitt, A. Sali. “Target Selection and Annotation for the Structural Genomics of the Amidohydrolase and Enolase Superfamilies”, Journal of Structural and Functional Genomics, 10 (2009) 107–125. PMC2693957
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
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.
43.
M. E. Glasner, N. Fayazmanesh, R. Chiang, A. Sakai, M. P. Jacobson, J. A. Gerlt, P. C. Babbitt. “Evolution of Structure and Function in the o-Succinylbenzoate Synthase/N-Acylamino Acid Racemase Family of the Enolase Superfamily.” Journal of Molecular Biology, 360 (2006) 228–250. Online
33.
C. Kalyanaraman, K. Bernacki, and M. P. Jacobson. “Virtual screening against highly charged active sites: Identifying substrates of alpha-beta barrel enzymes”, Biochemistry, 44 (2005) 2059–2071. [One of top 20 most accessed articles in Biochemistry in 2005.] Online
32.
V. C. Ruddat, R. Mogul, I. Chorny, C. Chen, N. Perrin, S. Whitman, V. Kenyon, M. P. Jacobson, C. F. Bernasconi, and T. R. Holman. “Tryptophan 500 and Arginine 707 Define Product and Substrate Active Site Binding in Soybean Lipoxygenase-1”, Biochemistry, 43 (2004) 13063–13071. Online
The Jacobson Laboratory at UCSF 