EFI - Training Resources: Training and Publications

This web resource is supported by a Research Resource from the National Institute of General Medical Sciences (R24GM141196-01).
The tools are available without charge or license to both academic and commercial users.
Option C now uses the sequences supplied in the FASTA file to calculate edge values and the IDs in the headers to retrieve node attribute information from UniProt. Like Option D, the user can specify that the input sequences are UniProt, UniRef90, or UniRef50 for retrieval of node attribute information.

833 Journal Articles

Wichelecki, D. J., Balthazor, B. M., Chau, A. C., Vetting, M. W., Fedorov, A. A., Fedorov, E. V., Lukk, T., Patskovsky, Y. V., Stead, M. B., Hillerich, B. S., Seidel, R. D., Almo, S. C., Gerlt, J. A., Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup. Biochemistry, 2014. 53(16): p. 2722-31. http://doi.org/10.1021/bi500264p
Wichelecki, D. J., Graff, D. C., Al-Obaidi, N., Almo, S. C., Gerlt, J. A., Identification of the in vivo function of the high-efficiency D-mannonate dehydratase in Caulobacter crescentus NA1000 from the enolase superfamily. Biochemistry, 2014. 53(25): p. 4087-9. http://doi.org/10.1021/bi500683x
Dunbar, K. L., Chekan, J. R., Cox, C. L., Burkhart, B. J., Nair, S. K., Mitchell, D. A., Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis. Nat Chem Biol, 2014. 10(10): p. 823-9. http://doi.org/10.1038/nchembio.1608
Vetting, M. W., Al-Obaidi, N., Zhao, S., San Francisco, B., Kim, J., Wichelecki, D. J., Bouvier, J. T., Solbiati, J. O., Vu, H., Zhang, X., Rodionov, D. A., Love, J. D., Hillerich, B. S., Seidel, R. D., Quinn, R. J., Osterman, A. L., Cronan, J. E., Jacobson, M. P., Gerlt, J. A., Almo, S. C., Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry, 2015. 54(3): p. 909-31. http://doi.org/10.1021/bi501388y
Rao, G., O'Dowd, B., Li, J., Wang, K., Oldfield, E., IspH–RPS1 and IspH–UbiA:“Rosetta stone” proteins. Chemical science, 2015. 6(12): p. 6813-6822. http://doi.org/10.1039/C5SC02600H
Roche, D., Brackenridge, D., McGuffin, L., Proteins and their interacting partners: An introduction to protein–ligand binding site prediction methods. International journal of molecular sciences, 2015. 16(12): p. 29829-29842. http://doi.org/10.3390/ijms161226202
San Francisco, B., Zhang, X., Whalen, K., Gerlt, J., A Novel Pathway for Bacterial Ethanolamine Metabolism. The FASEB Journal, 2015. 29(1_supplement): p. 573.45.
Anders, K., Essen, L., The family of phytochrome-like photoreceptors: diverse, complex and multi-colored, but very useful. Current Opinion in Structural Biology, 2015. 35: p. 7-16. http://doi.org/10.1016/j.sbi.2015.07.005
Zhang, X., Kumar, R., Vetting, M. W., Zhao, S., Jacobson, M. P., Almo, S. C., Gerlt, J. A., A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily. J Am Chem Soc, 2015. 137(4): p. 1388-91. http://doi.org/10.1021/ja5103986
Celis, A. I., DuBois, J. L., Substrate, product, and cofactor: The extraordinarily flexible relationship between the CDE superfamily and heme. Arch Biochem Biophys, 2015. 574: p. 3-17. http://doi.org/10.1016/j.abb.2015.03.004
Latham, J. A., Iavarone, A. T., Barr, I., Juthani, P. V., Klinman, J. P., PqqD is a novel peptide chaperone that forms a ternary complex with the radical S-adenosylmethionine protein PqqE in the pyrroloquinoline quinone biosynthetic pathway. J Biol Chem, 2015. 290(20): p. 12908-18. http://doi.org/10.1074/jbc.M115.646521
Liu, F., Geng, J., Gumpper, R. H., Barman, A., Davis, I., Ozarowski, A., Hamelberg, D., Liu, A., An Iron Reservoir to the Catalytic Metal: THE RUBREDOXIN IRON IN AN EXTRADIOL DIOXYGENASE. J Biol Chem, 2015. 290(25): p. 15621-34. http://doi.org/10.1074/jbc.M115.650259
Burkhart, B. J., Hudson, G. A., Dunbar, K. L., Mitchell, D. A., A prevalent peptide-binding domain guides ribosomal natural product biosynthesis. Nat Chem Biol, 2015. 11(8): p. 564-70. http://doi.org/10.1038/nchembio.1856
Cox, C. L., Doroghazi, J. R., Mitchell, D. A., The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles. BMC Genomics, 2015. 16(1): p. 778. http://doi.org/10.1186/s12864-015-2008-0
Wichelecki, D. J., Vetting, M. W., Chou, L., Al-Obaidi, N., Bouvier, J. T., Almo, S. C., Gerlt, J. A., ATP-binding Cassette (ABC) Transport System Solute-binding Protein-guided Identification of Novel d-Altritol and Galactitol Catabolic Pathways in Agrobacterium tumefaciens C58. J Biol Chem, 2015. 290(48): p. 28963-76. http://doi.org/10.1074/jbc.M115.686857
Petronikolou, N., Nair, S. K., Biochemical Studies of Mycobacterial Fatty Acid Methyltransferase: A Catalyst for the Enzymatic Production of Biodiesel. Chem Biol, 2015. 22(11): p. 1480-1490. http://doi.org/10.1016/j.chembiol.2015.09.011
Huang, H., Carter, M. S., Vetting, M. W., Al-Obaidi, N., Patskovsky, Y., Almo, S. C., Gerlt, J. A., A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis. J Am Chem Soc, 2015. 137(46): p. 14570-3. http://doi.org/10.1021/jacs.5b08968
Colin, P. Y., Kintses, B., Gielen, F., Miton, C. M., Fischer, G., Mohamed, M. F., Hyvonen, M., Morgavi, D. P., Janssen, D. B., Hollfelder, F., Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics. Nat Commun, 2015. 6: p. 10008. http://doi.org/10.1038/ncomms10008
Molloy, E. M., Tietz, J. I., Blair, P. M., Mitchell, D. A., Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products. Bioorganic & medicinal chemistry, 2016. 24(24): p. 6276-6290. http://doi.org/10.1016/j.bmc.2016.05.021
Plach, M. G., Reisinger, B., Sterner, R., Merkl, R., Long-term persistence of bi-functionality contributes to the robustness of microbial life through exaptation. PLoS genetics, 2016. 12(1): p. e1005836. http://doi.org/10.1371/journal.pgen.1005836
Thotsaporn, K., Tinikul, R., Maenpuen, S., Phonbuppha, J., Watthaisong, P., Chenprakhon, P., Chaiyen, P., Enzymes in the p-hydroxyphenylacetate degradation pathway of Acinetobacter baumannii. Journal of Molecular Catalysis B: Enzymatic, 2016. 134: p. 353-366. http://doi.org/10.1016/j.molcatb.2016.09.003
Kumar, G., Johnson, J. L., Frantom, P. A., Improving functional annotation in the DRE-TIM metallolyase superfamily through identification of active site fingerprints. Biochemistry, 2016. 55(12): p. 1863-1872. http://doi.org/10.1021/acs.biochem.5b01193
Ahmed, F. H., Mohamed, A. E., Carr, P. D., Lee, B. M., Condic‐Jurkic, K., O'Mara, M. L., Jackson, C. J., Rv2074 is a novel F420H2‐dependent biliverdin reductase in Mycobacterium tuberculosis. Protein Science, 2016. 25(9): p. 1692-1709. http://doi.org/10.1002/pro.2975
Atkinson, J. T., Campbell, I., Bennett, G. N., Silberg, J. J., Cellular assays for ferredoxins: a strategy for understanding electron flow through protein carriers that link metabolic pathways. Biochemistry, 2016. 55(51): p. 7047-7064. http://doi.org/10.1021/acs.biochem.6b00831
Ji, X., Li, Y., Xie, L., Lu, H., Ding, W., Zhang, Q., Expanding radical SAM chemistry by using radical addition reactions and SAM analogues. Angewandte Chemie International Edition, 2016. 55(39): p. 11845-11848. http://doi.org/10.1002/anie.201605917
Zhang, X., Carter, M. S., Vetting, M. W., San Francisco, B., Zhao, S., Al-Obaidi, N. F., Solbiati, J. O., Thiaville, J. J., de Crécy-Lagard, V., Jacobson, M. P., 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, 2016. 113(29): p. E4161-E4169. http://doi.org/10.1073/pnas.1605546113
Tietz, J.I., Mitchell, D.A., Using genomics for natural product structure elucidation. Current topics in medicinal chemistry, 2016. 16(15): p. 1645-1694. http://doi.org/10.2174/1568026616666151012111439
Prunetti, L., El Y. B., Schiavon, C. R., Kirkpatrick, E., Huang, L., Bailly, M., El B. M., Harrison, K., Gregory 3rd, J. F., Fiehn, O., Evidence that COG0325 proteins are involved in PLP homeostasis. Microbiology, 2016. 162(4): p. 694-706. http://doi.org/10.1099/mic.0.000255
Gerlt, J. A., Tools and strategies for discovering novel enzymes and metabolic pathways. Perspectives in science, 2016. 9: p. 24-32. http://doi.org/10.1016/j.pisc.2016.07.001
Colabroy, K. L., Tearing down to build up: Metalloenzymes in the biosynthesis lincomycin, hormaomycin and the pyrrolo [1,4]benzodiazepines. Biochim Biophys Acta, 2016. 1864(6): p. 724-737. http://doi.org/10.1016/j.bbapap.2016.03.001
Ding, W., Li, Q., Jia, Y., Ji, X., Qianzhu, H., Zhang, Q., Emerging Diversity of the Cobalamin-Dependent Methyltransferases Involving Radical-Based Mechanisms. Chembiochem, 2016. 17(13): p. 1191-7. http://doi.org/10.1002/cbic.201600107
Ghodge, S. V., Biernat, K. A., Bassett, S. J., Redinbo, M. R., Bowers, A. A., Post-translational Claisen Condensation and Decarboxylation en Route to the Bicyclic Core of Pantocin A. J Am Chem Soc, 2016. 138(17): p. 5487-90. http://doi.org/10.1021/jacs.5b13529
Machovina, M. M., Usselman, R. J., DuBois, J. L., Monooxygenase Substrates Mimic Flavin to Catalyze Cofactorless Oxygenations. J Biol Chem, 2016. 291(34): p. 17816-28. http://doi.org/10.1074/jbc.M116.730051
Rao, G., Oldfield, E., Structure and Function of Four Classes of the 4Fe-4S Protein, IspH. Biochemistry, 2016. 55(29): p. 4119-29. http://doi.org/10.1021/acs.biochem.6b00474
Desai, J., Liu, Y. L., Wei, H., Liu, W., Ko, T. P., Guo, R. T., Oldfield, E., Structure, Function, and Inhibition of Staphylococcus aureus Heptaprenyl Diphosphate Synthase. ChemMedChem, 2016. 11(17): p. 1915-23. http://doi.org/10.1002/cmdc.201600311
Ji, X., Liu, W. Q., Yuan, S., Yin, Y., Ding, W., Zhang, Q., Mechanistic study of the radical SAM-dependent amine dehydrogenation reactions. Chem Commun (Camb), 2016. 52(69): p. 10555-8. http://doi.org/10.1039/c6cc05661j
Zallot, R., Harrison, K. J., Kolaczkowski, B., de Crecy-Lagard, V., Functional Annotations of Paralogs: A Blessing and a Curse. Life (Basel), 2016. 6(3): p. 39. http://doi.org/10.3390/life6030039
Li, D., Moorman, R., Vanhercke, T., Petrie, J., Singh, S., Jackson, C. J., Classification and substrate head-group specificity of membrane fatty acid desaturases. Comput Struct Biotechnol J, 2016. 14: p. 341-349. http://doi.org/10.1016/j.csbj.2016.08.003
Davey, L., Halperin, S. A., Lee, S. F., Thiol-Disulfide Exchange in Gram-Positive Firmicutes. Trends Microbiol, 2016. 24(11): p. 902-915. http://doi.org/10.1016/j.tim.2016.06.010
Maxson, T., Tietz, J. I., Hudson, G. A., Guo, X. R., Tai, H. C., Mitchell, D. A., Targeting Reactive Carbonyls for Identifying Natural Products and Their Biosynthetic Origins. J Am Chem Soc, 2016. 138(46): p. 15157-15166. http://doi.org/10.1021/jacs.6b06848
Baier, F., Copp, J. N., Tokuriki, N., Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence-Function Relationships. Biochemistry, 2016. 55(46): p. 6375-6388. http://doi.org/10.1021/acs.biochem.6b00723
Dassama, L. M., Kenney, G. E., Ro, S. Y., Zielazinski, E. L., Rosenzweig, A. C., Methanobactin transport machinery. Proc Natl Acad Sci U S A, 2016. 113(46): p. 13027-13032. http://doi.org/10.1073/pnas.1603578113
Hao, Y., Pierce, E., Roe, D., Morita, M., McIntosh, J. A., Agarwal, V., Cheatham, T. E., 3rd, Schmidt, E. W., Nair, S. K., Molecular basis for the broad substrate selectivity of a peptide prenyltransferase. Proc Natl Acad Sci U S A, 2016. 113(49): p. 14037-14042. http://doi.org/10.1073/pnas.1609869113
Jia, B., Jia, X., Kim, K. H., Jeon, C. O., Integrative view of 2-oxoglutarate/Fe(II)-dependent oxygenase diversity and functions in bacteria. Biochim Biophys Acta Gen Subj, 2017. 1861(2): p. 323-334. http://doi.org/10.1016/j.bbagen.2016.12.001
Chekan, J. R., Koos, J. D., Zong, C., Maksimov, M. O., Link, A. J., Nair, S. K., Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates. J Am Chem Soc, 2016. 138(50): p. 16452-16458. http://doi.org/10.1021/jacs.6b10389
Bhandari, D. M., Fedoseyenko, D., Begley, T. P., Tryptophan Lyase (NosL): A Cornucopia of 5'-Deoxyadenosyl Radical Mediated Transformations. J Am Chem Soc, 2016. 138(50): p. 16184-16187. http://doi.org/10.1021/jacs.6b06139
Ortega, M. A., Cogan, D. P., Mukherjee, S., Garg, N., Li, B., Thibodeaux, G. N., Maffioli, S. I., Donadio, S., Sosio, M., Escano, J., Smith, L., Nair, S. K., van der Donk, W. A., Two Flavoenzymes Catalyze the Post-Translational Generation of 5-Chlorotryptophan and 2-Aminovinyl-Cysteine during NAI-107 Biosynthesis. ACS Chem Biol, 2017. 12(2): p. 548-557. http://doi.org/10.1021/acschembio.6b01031
McFarland, B. J., Online Tools for Teaching Large Laboratory Courses: How the GENI Website Facilitates Authentic Research. Teaching and the Internet: The Application of Web Apps, Networking, and Online Tech for Chemistry Education, 2017. http://doi.org/10.1021/bk-2017-1270.ch008
Hopkins, D. H., Fraser, N. J., Mabbitt, P. D., Carr, P. D., Oakeshott, J. G., Jackson, C. J., Structure of an insecticide sequestering carboxylesterase from the disease vector Culex quinquefasciatus: what makes an enzyme a good insecticide sponge?. Biochemistry, 2017. 56(41): p. 5512-5525. http://doi.org/10.1021/acs.biochem.7b00774
Holliday, G. L., Brown, S. D., Akiva, E., Mischel, D., Hicks, M. A., Morris, J. H., Huang, C. C., Meng, E. C., Pegg, S. C., Ferrin, T. E., Biocuration in the structure–function linkage database: the anatomy of a superfamily. Database, 2017. 2017. http://doi.org/10.1093/database/bax045
Wang, H., Chen, X., Li, C., Liu, Y., Yang, F., Wang, C., Sequence-based prediction of cysteine reactivity using machine learning. Biochemistry, 2017. 57(4): p. 451-460. http://doi.org/10.1021/acs.biochem.7b00897
Lohans, C. T., Wang, D. Y., Wang, J., Hamed, R. B., Schofield, C. J., Crotonases: nature’s exceedingly convertible catalysts. ACS Catalysis, 2017. 7(10): p. 6587-6599. http://doi.org/10.1021/acscatal.7b01699
Orth, C., Niemann, N., Hennig, L., Essen, L., Batschauer, A., Hyperactivity of the Arabidopsis cryptochrome (cry1) L407F mutant is caused by a structural alteration close to the cry1 ATP-binding site. Journal of Biological Chemistry, 2017. 292(31): p. 12906-12920. http://doi.org/10.1074/jbc.M117.788869
Holliday, G. L., Davidson, R., Akiva, E., Babbitt, P. C., Evaluating functional annotations of enzymes using the gene ontology. The Gene Ontology Handbook, 2017. http://doi.org/10.1007/978-1-4939-3743-1_9
Wang, M., Moynié, L., Harrison, P. J., Kelly, V., Piper, A., Naismith, J. H., Campopiano, D. J., Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters. Nature chemical biology, 2017. 13(6): p. 660. http://doi.org/10.1038/nchembio.2361
Bearne, S. L., The interdigitating loop of the enolase superfamily as a specificity binding determinant or ‘flying buttress’. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 2017. 1865(5): p. 619-630. http://doi.org/10.1016/j.bbapap.2017.02.006
Zallot, R., Yuan, Y., de Crécy-Lagard, V., The Escherichia coli COG1738 member YhhQ is involved in 7-cyanodeazaguanine (preQ0) transport. Biomolecules, 2017. 7(1): p. 12. http://doi.org/10.3390/biom7010012
Ney, B., Ahmed, F. H., Carere, C. R., Biswas, A., Warden, A. C., Morales, S. E., Pandey, G., Watt, S. J., Oakeshott, J. G., Taylor, M. C., The methanogenic redox cofactor F 420 is widely synthesized by aerobic soil bacteria. The ISME journal, 2017. 11(1): p. 125. http://doi.org/10.1038/ismej.2016.100
Cogan, D. P., Hudson, G. A., Zhang, Z., Pogorelov, T. V., van der Donk, W. A., Mitchell, D. A., Nair, S. K., Structural insights into enzymatic [4+ 2] aza-cycloaddition in thiopeptide antibiotic biosynthesis. Proceedings of the National Academy of Sciences, 2017. 114(49): p. 12928-12933. http://doi.org/10.1073/pnas.1716035114
Macaisne, N., Liu, F., Scornet, D., Peters, A. F., Lipinska, A., Perrineau, M. M., Henry, A., Strittmatter, M., Coelho, S. M., Cock, J. M., The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes. Development, 2017. 144(3): p. 409-418. http://doi.org/10.1242/dev.141523
Repka, L. M., Chekan, J. R., Nair, S. K., van der Donk, W. A., Mechanistic Understanding of Lanthipeptide Biosynthetic Enzymes. Chem Rev, 2017. 117(8): p. 5457-5520. http://doi.org/10.1021/acs.chemrev.6b00591
Pimviriyakul, P., Thotsaporn, K., Sucharitakul, J., Chaiyen, P., Kinetic Mechanism of the Dechlorinating Flavin-dependent Monooxygenase HadA. J Biol Chem, 2017. 292(12): p. 4818-4832. http://doi.org/10.1074/jbc.M116.774448
Erb, T. J., Jones, P. R., Bar-Even, A., Synthetic metabolism: metabolic engineering meets enzyme design. Curr Opin Chem Biol, 2017. 37: p. 56-62. http://doi.org/10.1016/j.cbpa.2016.12.023
Pornsuwan, S., Maenpuen, S., Kamutira, P., Watthaisong, P., Thotsaporn, K., Tongsook, C., Juttulapa, M., Nijvipakul, S., Chaiyen, P., 3,4-Dihydroxyphenylacetate 2,3-dioxygenase from Pseudomonas aeruginosa: An Fe(II)-containing enzyme with fast turnover. PLoS One, 2017. 12(2): p. e0171135. http://doi.org/10.1371/journal.pone.0171135
Glasner, M. E., Finding enzymes in the gut metagenome. Science, 2017. 355(6325): p. 577-578. http://doi.org/10.1126/science.aam7446
Levin, B. J., Huang, Y. Y., Peck, S. C., Wei, Y., Martinez-Del C. A., Marks, J. A., Franzosa, E. A., Huttenhower, C., Balskus, E. P., A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science, 2017. 355(6325): p. eaai8386. http://doi.org/10.1126/science.aai8386
Jia, B., Jia, X., Hyun K. K., Ji P. Z., Kang, M. S., Ok J. C., Evolutionary, computational, and biochemical studies of the salicylaldehyde dehydrogenases in the naphthalene degradation pathway. Sci Rep, 2017. 7: p. 43489. http://doi.org/10.1038/srep43489
Tietz, J. I., Schwalen, C. J., Patel, P. S., Maxson, T., Blair, P. M., Tai, H. C., Zakai, U. I., Mitchell, D. A., A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nat Chem Biol, 2017. 13(5): p. 470-478. http://doi.org/10.1038/nchembio.2319
Giessen, T. W., Silver, P. A., Widespread distribution of encapsulin nanocompartments reveals functional diversity. Nat Microbiol, 2017. 2(6): p. 17029. http://doi.org/10.1038/nmicrobiol.2017.29
Hetrick, K. J., van der Donk, W. A., Ribosomally synthesized and post-translationally modified peptide natural product discovery in the genomic era. Curr Opin Chem Biol, 2017. 38: p. 36-44. http://doi.org/10.1016/j.cbpa.2017.02.005
Schwalen, C. J., Feng, X., Liu, W., O. D. B., Ko, T. P., Shin, C. J., Guo, R. T., Mitchell, D. A., Oldfield, E., Head-to-Head Prenyl Synthases in Pathogenic Bacteria. Chembiochem, 2017. 18(11): p. 985-991. http://doi.org/10.1002/cbic.201700099
Ahmed, M. N., Reyna-Gonzalez, E., Schmid, B., Wiebach, V., Sussmuth, R. D., Dittmann, E., Fewer, D. P., Phylogenomic Analysis of the Microviridin Biosynthetic Pathway Coupled with Targeted Chemo-Enzymatic Synthesis Yields Potent Protease Inhibitors. ACS Chem Biol, 2017. 12(6): p. 1538-1546. http://doi.org/10.1021/acschembio.7b00124
Estrada, P., Manandhar, M., Dong, S. H., Deveryshetty, J., Agarwal, V., Cronan, J. E., Nair, S. K., The pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes. Nat Chem Biol, 2017. 13(6): p. 668-674. http://doi.org/10.1038/nchembio.2359
Haase, E. M., Kou, Y., Sabharwal, A., Liao, Y. C., Lan, T., Lindqvist, C., Scannapieco, F. A., Comparative genomics and evolution of the amylase-binding proteins of oral streptococci. BMC Microbiol, 2017. 17(1): p. 94. http://doi.org/10.1186/s12866-017-1005-7
Blin, K., Wolf, T., Chevrette, M. G., Lu, X., Schwalen, C. J., Kautsar, S. A., Suarez D. H. G., de Los Santos, E. L. C., Kim, H. U., Nave, M., Dickschat, J. S., Mitchell, D. A., Shelest, E., Breitling, R., Takano, E., Lee, S. Y., Weber, T., Medema, M. H., antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res, 2017. 45(W1): p. W36-W41. http://doi.org/10.1093/nar/gkx319
Kandlinger, F., Plach, M. G., Merkl, R., AGeNNT: annotation of enzyme families by means of refined neighborhood networks. BMC Bioinformatics, 2017. 18(1): p. 274. http://doi.org/10.1186/s12859-017-1689-6
Wagner, D. T., Zeng, J., Bailey, C. B., Gay, D. C., Yuan, F., Manion, H. R., Keatinge-Clay, A. T., Structural and Functional Trends in Dehydrating Bimodules from trans-Acyltransferase Polyketide Synthases. Structure, 2017. 25(7): p. 1045-1055 e2. http://doi.org/10.1016/j.str.2017.05.011
Benjdia, A., Guillot, A., Ruffie, P., Leprince, J., Berteau, O., Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis. Nat Chem, 2017. 9(7): p. 698-707. http://doi.org/10.1038/nchem.2714
Koppel, N., Maini R. V., Balskus, E. P., Chemical transformation of xenobiotics by the human gut microbiota. Science, 2017. 356(6344): p. eaag2770. http://doi.org/10.1126/science.aag2770
Zhong, G., Zhao, Q., Zhang, Q., Liu, W., 4-alkyl-L-(Dehydro)proline biosynthesis in actinobacteria involves N-terminal nucleophile-hydrolase activity of gamma-glutamyltranspeptidase homolog for C-C bond cleavage. Nat Commun, 2017. 8: p. 16109. http://doi.org/10.1038/ncomms16109
Chowdhary, J., Loffler, F. E., Smith, J. C., Community detection in sequence similarity networks based on attribute clustering. PLoS One, 2017. 12(7): p. e0178650. http://doi.org/10.1371/journal.pone.0178650
Essen, L. O., Franz, S., Banerjee, A., Structural and evolutionary aspects of algal blue light receptors of the cryptochrome and aureochrome type. J Plant Physiol, 2017. 217: p. 27-37. http://doi.org/10.1016/j.jplph.2017.07.005
Rudolf, J. D., Chang, C. Y., Ma, M., Shen, B., Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep, 2017. 34(9): p. 1141-1172. http://doi.org/10.1039/c7np00034k
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