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2022 Journal Article Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structuresPan, Qisheng, Nguyen, Thanh Binh, Ascher, David B and Pires, Douglas E V (2022). Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. Briefings in Bioinformatics, 23 (2) bbac025. doi: 10.1093/bib/bbac025 |
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2022 Journal Article Known allosteric proteins have central roles in genetic diseaseAbrusán, György, Ascher, David B. and Inouye, Michael (2022). Known allosteric proteins have central roles in genetic disease. PLoS Computational Biology, 18 (2) e1009806, 1-28. doi: 10.1371/journal.pcbi.1009806 |
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2022 Journal Article epitope3D: a machine learning method for conformational B-cell epitope predictionda Silva, Bruna Moreira, Myung, YooChan, Ascher, David B. and Pires, Douglas E. V. (2022). epitope3D: a machine learning method for conformational B-cell epitope prediction. Briefings in Bioinformatics, 23 (1) bbab423, 1-8. doi: 10.1093/bib/bbab423 |
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2022 Journal Article Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteriaSharma, Mahima, Lingford, James P., Petricevic, Marija, Snow, Alexander J. D., Zhang, Yunyang, Järvå, Michael A., Mui, Janice W.-Y., Scott, Nichollas E., Saunders, Eleanor C., Mao, Runyu, Epa, Ruwan, da Silva, Bruna M., Pires, Douglas E. V., Ascher, David B., McConville, Malcolm J., Davies, Gideon J., Williams, Spencer J. and Goddard-Borger, Ethan D. (2022). Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Proceedings of the National Academy of Sciences, 119 (4), e2116022119. doi: 10.1073/pnas.2116022119 |
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2022 Journal Article CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring functionNguyen, Thanh Binh, Pires, Douglas E. V. and Ascher, David B. (2022). CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function. Briefings in Bioinformatics, 23 (1) bbab512, 1-8. doi: 10.1093/bib/bbab512 |
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2021 Journal Article TSMDA: Target and symptom-based computational model for miRNA-disease-association predictionUthayopas, Korawich, de Sá, Alex G.C., Alavi, Azadeh, Pires, Douglas E.V. and Ascher, David B. (2021). TSMDA: Target and symptom-based computational model for miRNA-disease-association prediction. Molecular Therapy - Nucleic Acids, 26, 536-546. doi: 10.1016/j.omtn.2021.08.016 |
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2021 Journal Article PdCSM-PPI: Using graph-based signatures to identify protein-protein interaction inhibitorsRodrigues, Carlos H.M., Pires, Douglas E.V. and Ascher, David B. (2021). PdCSM-PPI: Using graph-based signatures to identify protein-protein interaction inhibitors. Journal of Chemical Information and Modeling, 61 (11), 5438-5445. doi: 10.1021/acs.jcim.1c01135 |
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2021 Journal Article mmCSM-NA: accurately predicting effects of single and multiple mutations on protein–nucleic acid binding affinityNguyen, Thanh Binh, Myung, Yoochan, de Sá, Alex G. C., Pires, Douglas E. V. and Ascher, David B. (2021). mmCSM-NA: accurately predicting effects of single and multiple mutations on protein–nucleic acid binding affinity. NAR Genomics and Bioinformatics, 3 (4) lqab109, lqab109. doi: 10.1093/nargab/lqab109 |
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2021 Journal Article CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring functionMyung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2021). CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring function. Bioinformatics, 38 (4), 1141-1143. doi: 10.1093/bioinformatics/btab762 |
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2021 Journal Article A novel deep intronic variant strongly associates with AlkaptonuriaLai, Chien-Yi, Tsai, I-Jung, Chiu, Pao-Chin, Ascher, David B., Chien, Yin-Hsiu, Huang, Yu-Hsuan, Lin, Yi-Lin, Hwu, Wuh-Liang and Lee, Ni-Chung (2021). A novel deep intronic variant strongly associates with Alkaptonuria. npj Genomic Medicine, 6 (1) 89, 89. doi: 10.1038/s41525-021-00252-2 |
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2021 Journal Article Definition of the immune evasion-replication interface of rabies virus P proteinZhan, Jingyu, Harrison, Angela R., Portelli, Stephanie, Nguyen, Thanh Binh, Kojima, Isshu, Zheng, Siqiong, Yan, Fei, Masatani, Tatsunori, Rawlinson, Stephen M., Sethi, Ashish, Ito, Naoto, Ascher, David B., Moseley, Gregory W. and Gooley, Paul R. (2021). Definition of the immune evasion-replication interface of rabies virus P protein. PLOS Pathogens, 17 (7) e1009729, 1-27. doi: 10.1371/journal.ppat.1009729 |
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2021 Journal Article MTR3D: identifying regions within protein tertiary structures under purifying selectionSilk, Michael, Pires, Douglas E V, Rodrigues, Carlos H M, D’Souza, Elston N, Olshansky, Moshe, Thorne, Natalie and Ascher, David B (2021). MTR3D: identifying regions within protein tertiary structures under purifying selection. Nucleic Acids Research, 49 (W1), W438-W445. doi: 10.1093/nar/gkab428 |
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2021 Journal Article pdCSM-cancer: using graph-based signatures to identify small molecules with anticancer propertiesAl-Jarf, Raghad, de Sá, Alex G. C., Pires, Douglas E. V. and Ascher, David B. (2021). pdCSM-cancer: using graph-based signatures to identify small molecules with anticancer properties. Journal of Chemical Information and Modeling, 61 (7), 3314-3322. doi: 10.1021/acs.jcim.1c00168 |
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2021 Journal Article mmCSM-PPI: predicting the effects of multiple point mutations on protein–protein interactionsRodrigues, Carlos H. M., Pires, Douglas E. V. and Ascher, David B. (2021). mmCSM-PPI: predicting the effects of multiple point mutations on protein–protein interactions. Nucleic Acids Research, 49 (W1), W417-W424. doi: 10.1093/nar/gkab273 |
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2021 Journal Article Mercury methylation by metabolically versatile and cosmopolitan marine bacteriaLin, Heyu, Ascher, David B., Myung, Yoochan, Lamborg, Carl H., Hallam, Steven J., Gionfriddo, Caitlin M., Holt, Kathryn E. and Moreau, John W. (2021). Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. The ISME Journal, 15 (6), 1810-1825. doi: 10.1038/s41396-020-00889-4 |
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2021 Journal Article Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resourcePortelli, Stephanie, Olshansky, Moshe, Rodrigues, Carlos H. M., D’Souza, Elston N., Myung, Yoochan, Silk, Michael, Alavi, Azadeh, Pires, Douglas E. V. and Ascher, David B. (2021). Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 53 (2), 254-254. doi: 10.1038/s41588-020-00775-x |
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2021 Book Chapter Identifying genotype-phenotype correlations via integrative mutation analysisAirey, Edward, Portelli, Stephanie, Xavier, Joicymara S, Myung, Yoo Chan, Silk, Michael, Karmakar, Malancha, Velloso, João P L, Rodrigues, Carlos H M, Parate, Hardik H, Garg, Anjali, Al-Jarf, Raghad, Barr, Lucy, Geraldo, Juliana A, Rezende, Pâmela M, Pires, Douglas E V and Ascher, David B (2021). Identifying genotype-phenotype correlations via integrative mutation analysis. Artificial neural networks. (pp. 1-32) edited by Hugh Cartwright. New York, NY, United States: Humana. doi: 10.1007/978-1-0716-0826-5_1 |
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2021 Journal Article Unveiling six potent and highly selective antileishmanial agents via the open source compound collection ‘Pathogen Box’ against antimony-sensitive and -resistant Leishmania braziliensisSouza Silva, Juliano A., Tunes, Luiza G., Coimbra, Roney S., Ascher, David B., Pires, Douglas E.V. and Monte-Neto, Rubens L. (2021). Unveiling six potent and highly selective antileishmanial agents via the open source compound collection ‘Pathogen Box’ against antimony-sensitive and -resistant Leishmania braziliensis. Biomedicine and Pharmacotherapy, 133 111049, 111049. doi: 10.1016/j.biopha.2020.111049 |
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2021 Journal Article Distinguishing between PTEN clinical phenotypes through mutation analysisPortelli, Stephanie, Barr, Lucy, de Sá, Alex G.C., Pires, Douglas E.V. and Ascher, David B. (2021). Distinguishing between PTEN clinical phenotypes through mutation analysis. Computational and Structural Biotechnology Journal, 19, 3097-3109. doi: 10.1016/j.csbj.2021.05.028 |
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2021 Journal Article Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinaseZhou, Yunzhuo, Portelli, Stephanie, Pat, Megan, Rodrigues, Carlos H.M., Nguyen, Thanh-Binh, Pires, Douglas E.V. and Ascher, David B. (2021). Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase. Computational and Structural Biotechnology Journal, 19, 5381-5391. doi: 10.1016/j.csbj.2021.09.016 |
