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2020 Journal Article Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase inVedithi, Sundeep Chaitanya, Rodrigues, Carlos H. M., Portelli, Stephanie, Skwark, Marcin J., Das, Madhusmita, Ascher, David B., Blundell, Tom L. and Malhotra, Sony (2020). Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in . Computational and Structural Biotechnology Journal, 18, 271-286. doi: 10.1016/j.csbj.2020.01.002 |
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2020 Journal Article Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH)Trapero, Ana, Pacitto, Angela, Chan, Daniel Shiu-Hin, Abell, Chris, Blundell, Tom L., Ascher, David B. and Coyne, Anthony G. (2020). Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH). Bioorganic and Medicinal Chemistry Letters, 30 (2) 126792, 126792. doi: 10.1016/j.bmcl.2019.126792 |
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2020 Journal Article Combining structure and genomics to understand antimicrobial resistanceTunstall, Tanushree, Portelli, Stephanie, Phelan, Jody, Clark, Taane G., Ascher, David B. and Furnham, Nicholas (2020). Combining structure and genomics to understand antimicrobial resistance. Computational and Structural Biotechnology Journal, 18, 3377-3394. doi: 10.1016/j.csbj.2020.10.017 |
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2020 Book Chapter A comprehensive computational platform to guide drug development using graph-based signature methodsPires, Douglas E. V., Portelli, Stephanie, Rezende, Pâmela M., Veloso, Wandré N. P., Xavier, Joicymara S., Karmakar, Malancha, Myung, Yoochan, Linhares, João P. V., Rodrigues, Carlos H. M., Silk, Michael and Ascher, David B. (2020). A comprehensive computational platform to guide drug development using graph-based signature methods. Structural bioinformatics: methods and protocols. (pp. 91-106) New York, NY, United States: Humana. doi: 10.1007/978-1-0716-0270-6_7 |
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2019 Journal Article Hyper transmission of Beijing lineage Mycobacterium tuberculosis: systematic review and meta-analysisKarmakar, Malancha, Trauer, James M, Ascher, David B and Denholm, Justin T (2019). Hyper transmission of Beijing lineage Mycobacterium tuberculosis: systematic review and meta-analysis. The Journal of Infection, 79 (6), 572-581. doi: 10.1016/j.jinf.2019.09.016 |
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2019 Journal Article dendPoint: a web resource for dendrimer pharmacokinetics investigation and predictionKaminskas, Lisa M., Pires, Douglas E. V. and Ascher, David B. (2019). dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction. Scientific Reports, 9 (1) 15465, 15465. doi: 10.1038/s41598-019-51789-3 |
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2019 Journal Article Large expert-curated database for benchmarking document similarity detection in biomedical literature searchBrown, Peter, Tan, Aik-Choon, El-Esawi, Mohamed A., Liehr, Thomas, Blanck, Oliver, Gladue, Douglas P., Almeida, Gabriel M. F., Cernava, Tomislav, Sorzano, Carlos O., Yeung, Andy W. K., Engel, Michael S., Chandrasekaran, Arun Richard, Muth, Thilo, Staege, Martin S., Daulatabad, Swapna V., Widera, Darius, Zhang, Junpeng, Meule, Adrian, Honjo, Ken, Pourret, Olivier, Yin, Cong-Cong, Zhang, Zhongheng, Cascella, Marco, Flegel, Willy A., Goodyear, Carl S., van Raaij, Mark J., Bukowy-Bieryllo, Zuzanna, Campana, Luca G., Kurniawan, Nicholas A. ... RELISH Consortium (2019). Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database-The Journal of Biological Databases and Curation, 2019 baz085, 1-67. doi: 10.1093/database/baz085 |
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2019 Journal Article Nedd8 hydrolysis by UCH proteases in Plasmodium parasitesKarpiyevich, Maryia, Adjalley, Sophie, Mol, Marco, Ascher, David B., Mason, Bethany, van der Heden van Noort, Gerbrand J., Laman, Heike, Ovaa, Huib, Lee, Marcus C. S. and Artavanis-Tsakonas, Katerina (2019). Nedd8 hydrolysis by UCH proteases in Plasmodium parasites. PLoS Pathogens, 15 (10), e1008086. doi: 10.1371/journal.ppat.1008086 |
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2019 Journal Article ProCarbDB: a database of carbohydrate-binding proteinsCopoiu, Liviu, Torres, Pedro H M, Ascher, David B, Blundell, Tom L and Malhotra, Sony (2019). ProCarbDB: a database of carbohydrate-binding proteins. Nucleic Acids Research, 48 (D1), D368-D375. doi: 10.1093/nar/gkz860 |
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2019 Journal Article A family of dual-activity glycosyltransferase-phosphorylases mediates mannogen turnover and virulence in Leishmania parasitesSernee, M. Fleur, Ralton, Julie E., Nero, Tracy L., Sobala, Lukasz F., Kloehn, Joachim, Vieira-Lara, Marcel A., Cobbold, Simon A., Stanton, Lauren, Pires, Douglas E. V., Hanssen, Eric, Males, Alexandra, Ward, Tom, Bastidas, Laurence M., van der Peet, Phillip L., Parker, Michael W., Ascher, David B., Williams, Spencer J., Davies, Gideon J. and McConville, Malcolm J. (2019). A family of dual-activity glycosyltransferase-phosphorylases mediates mannogen turnover and virulence in Leishmania parasites. Cell Host and Microbe, 26 (3), 385-399.e9. doi: 10.1016/j.chom.2019.08.009 |
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2019 Journal Article Synthesis and structure-activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDHSingh, Vinayak, Pacitto, Angela, Donini, Stefano, Ferraris, Davide M, Boros, Sándor, Illyés, Eszter, Szokol, Bálint, Rizzi, Menico, Blundell, Tom L, Ascher, David B, Pato, Janos and Mizrahi, Valerie (2019). Synthesis and structure-activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH. European Journal of Medicinal Chemistry, 174, 309-329. doi: 10.1016/j.ejmech.2019.04.027 |
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2019 Journal Article mCSM-PPI2: predicting the effects of mutations on protein–protein interactionsRodrigues, Carlos H. M., Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2019). mCSM-PPI2: predicting the effects of mutations on protein–protein interactions. Nucleic Acids Research, 47 (W1), W338-W344. doi: 10.1093/nar/gkz383 |
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2019 Journal Article MTR-Viewer: identifying regions within genes under purifying selectionSilk, Michael, Petrovski, Slavé and Ascher, David B (2019). MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Research, 47 (W1), W121-W126. doi: 10.1093/nar/gkz457 |
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2019 Journal Article Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKUAscher, David B, Spiga, Ottavia, Sekelska, Martina, Pires, Douglas E V, Bernini, Andrea, Tiezzi, Monica, Kralovicova, Jana, Borovska, Ivana, Soltysova, Andrea, Olsson, Birgitta, Galderisi, Silvia, Cicaloni, Vittoria, Ranganath, Lakshminarayan, Santucci, Annalisa and Zatkova, Andrea (2019). Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU. European Journal of Human Genetics : EJHG, 27 (6), 888-902. doi: 10.1038/s41431-019-0354-0 |
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2019 Journal Article Empirical ways to identify novel Bedaquiline resistance mutations in AtpEKarmakar, Malancha, Rodrigues, Carlos H M, Holt, Kathryn E, Dunstan, Sarah J, Denholm, Justin and Ascher, David B (2019). Empirical ways to identify novel Bedaquiline resistance mutations in AtpE. PloS one, 14 (5) e0217169, e0217169. doi: 10.1371/journal.pone.0217169 |
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2019 Journal Article Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulationsJatana, Nidhi, Ascher, David B., Pires, Douglas E.V., Gokhale, Rajesh S. and Thukral, Lipi (2019). Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations. Autophagy, 16 (2), 239-255. doi: 10.1080/15548627.2019.1606636 |
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2019 Journal Article A 30 kDa polyethylene glycol-enfuvirtide complex enhances the exposure of enfuvirtide in lymphatic viral reservoirs in ratsKaminskas, Lisa M., Williams, Charlotte C., Leong, Nathania J., Chan, Linda J., Butcher, Neville J., Feeney, Orlagh M., Porter, Christopher J.H., Tyssen, David, Tachedjian, Gilda and Ascher, David B. (2019). A 30 kDa polyethylene glycol-enfuvirtide complex enhances the exposure of enfuvirtide in lymphatic viral reservoirs in rats. European Journal of Pharmaceutics and Biopharmaceutics, 137, 218-226. doi: 10.1016/j.ejpb.2019.03.008 |
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2019 Book Chapter Exploring protein supersecondary structure through changes in protein folding, stability, and flexibilityPires, Douglas E. V., Rodrigues, Carlos H. M., Albanaz, Amanda T. S., Karmakar, Malancha, Myung, Yoochan, Xavier, Joicymara, Michanetzi, Eleni-Maria, Portelli, Stephanie and Ascher, David B. (2019). Exploring protein supersecondary structure through changes in protein folding, stability, and flexibility. Protein Supersecondary Structures: Methods and Protocols. (pp. 173-185) edited by Alexander E. Kister. New York, NY, United States: Springer. doi: 10.1007/978-1-4939-9161-7_9 |
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2018 Journal Article Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosisPortelli, Stephanie, Phelan, Jody E., Ascher, David B., Clark, Taane G. and Furnham, Nicholas (2018). Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. Scientific Reports, 8 (1) 15356. doi: 10.1038/s41598-018-33370-6 |
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2018 Journal Article Structural and biochemical insights into the function and evolution of sulfoquinovosidasesAbayakoon, Palika, Jin, Yi, Lingford, James P., Petricevic, Marija, John, Alan, Ryan, Eileen, Wai-Ying Mui, Janice, Pires, Douglas E.V., Ascher, David B., Davies, Gideon J., Goddard-Borger, Ethan D. and Williams, Spencer J. (2018). Structural and biochemical insights into the function and evolution of sulfoquinovosidases. ACS Central Science, 4 (9), 1266-1273. doi: 10.1021/acscentsci.8b00453 |
