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2022 Journal Article Identifying the molecular drivers of ALS-implicated missense mutationsPortelli, Stephanie, Albanaz, Amanda, Pires, Douglas Eduardo Valente and Ascher, David Benjamin (2022). Identifying the molecular drivers of ALS-implicated missense mutations. Journal of Medical Genetics, 60 (5) 108798, 1-7. doi: 10.1136/jmg-2022-108798 |
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2022 Journal Article VIVID: a web application for variant interpretation and visualisation in multidimensional analysesTichkule, Swapnil, Myung, Yoochan, Naung, Myo T., Ansell, Brendan R. E., Guy, Andrew J., Srivastava, Namrata, Mehra, Somya, Cacciò, Simone M, Mueller, Ivo, Barry, Alyssa E, van Oosterhout, Cock, Pope, Bernard, Ascher, David B and Jex, Aaron R (2022). VIVID: a web application for variant interpretation and visualisation in multidimensional analyses. Molecular Biology and Evolution, 39 (9) msac196. doi: 10.1093/molbev/msac196 |
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2022 Journal Article Sequence grammar underlying the unfolding and phase separation of globular proteinsRuff, Kiersten M., Choi, Yoon Hee, Cox, Dezerae, Ormsby, Angelique R., Myung, Yoochan, Ascher, David B., Radford, Sheena E., Pappu, Rohit V. and Hatters, Danny M. (2022). Sequence grammar underlying the unfolding and phase separation of globular proteins. Molecular Cell, 82 (17), 3193-3208.e8. doi: 10.1016/j.molcel.2022.06.024 |
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2022 Journal Article GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithmsPaiva, Vinícius A., Mendonça, Murillo V., Silveira, Sabrina A., Ascher, David B., Pires, Douglas E. V. and Izidoro, Sandro C. (2022). GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms. Briefings in Bioinformatics, 23 (5) bbac178, 1-9. doi: 10.1093/bib/bbac178 |
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2022 Journal Article toxCSM: comprehensive prediction of small molecule toxicity profilesde Sá, Alex G.C., Long, Yangyang, Portelli, Stephanie, Pires, Douglas E.V. and Ascher, David B. (2022). toxCSM: comprehensive prediction of small molecule toxicity profiles. Briefings in Bioinformatics, 23 (5) bbac337, 1-11. doi: 10.1093/bib/bbac337 |
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2022 Journal Article Use of cluster analysis to characterise aortic stenosis phenotypes with treatable and untreatable riskSen, J., Pires, D., de Sá, A., Ascher, D., Wahir, S. and Marwick, T. (2022). Use of cluster analysis to characterise aortic stenosis phenotypes with treatable and untreatable risk. Heart, Lung and Circulation, 31, S44-S45. doi: 10.1016/j.hlc.2022.06.016 |
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2022 Journal Article HGDiscovery: an online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenaseKarmakar, Malancha, Cicaloni, Vittoria, Rodrigues, Carlos H. M., Spiga, Ottavia, Santucci, Annalisa and Ascher, David B. (2022). HGDiscovery: an online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase. Current Research in Structural Biology, 4, 271-277. doi: 10.1016/j.crstbi.2022.08.001 |
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2022 Journal Article CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learningRodrigues, Carlos H. M. and Ascher, David B (2022). CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. Nucleic Acids Research, 50 (W1), W204-W209. doi: 10.1093/nar/gkac381 |
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2022 Journal Article Structural landscapes of PPI interfacesRodrigues, Carlos H. M., Pires, Douglas E. V., Blundell, Tom L. and Ascher, David B. (2022). Structural landscapes of PPI interfaces. Briefings in Bioinformatics, 23 (4) bbac165, 1-10. doi: 10.1093/bib/bbac165 |
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2022 Journal Article Evaluating hierarchical machine learning approaches to classify biological databasesRezende, Pâmela M., Xavier, Joicymara S., Ascher, David B., Fernandes, Gabriel R. and Pires, Douglas E. V. (2022). Evaluating hierarchical machine learning approaches to classify biological databases. Briefings in Bioinformatics, 23 (4) bbac216, 1-14. doi: 10.1093/bib/bbac216 |
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2022 Journal Article cropCSM: designing safe and potent herbicides with graph-based signaturesPires, Douglas E V, Stubbs, Keith A, Mylne, Joshua S and Ascher, David B (2022). cropCSM: designing safe and potent herbicides with graph-based signatures. Briefings in Bioinformatics, 23 (2) bbac042. doi: 10.1093/bib/bbac042 |
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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 |
