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2023 Journal Article embryoTox: using graph-based signatures to predict the teratogenicity of small moleculesAljarf, Raghad, Tang, Simon, Pires, Douglas E. V. and Ascher, David B. (2023). embryoTox: using graph-based signatures to predict the teratogenicity of small molecules. Journal of Chemical Information and Modeling, 63 (2), 432-441. doi: 10.1021/acs.jcim.2c00824 |
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2023 Journal Article DockNet: high-throughput protein–protein interface contact predictionWilliams, Nathan P., Rodrigues, Carlos H. M., Truong, Jia, Ascher, David B. and Holien, Jessica K. (2023). DockNet: high-throughput protein–protein interface contact prediction. Bioinformatics, 39 (1) btac797, 1-3. doi: 10.1093/bioinformatics/btac797 |
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2022 Journal Article SARS-CoV-2 Africa dashboard for real-time COVID-19 informationXavier, Joicymara S., Moir, Monika, Tegally, Houriiyah, Sitharam, Nikita, Abdool Karim, Wasim, San, James E., Linhares, Joana, Wilkinson, Eduan, Ascher, David B., Baxter, Cheryl, Pires, Douglas E. V. and de Oliveira, Tulio (2022). SARS-CoV-2 Africa dashboard for real-time COVID-19 information. Nature Microbiology, 8 (1), 1-4. doi: 10.1038/s41564-022-01276-9 |
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2022 Journal Article A bias of Asparagine to Lysine mutations in SARS-CoV-2 outside the receptor binding domain affects protein flexibilityBoer, Jennifer C., Pan, Qisheng, Holien, Jessica K., Nguyen, Thanh-Binh, Ascher, David B. and Plebanski, Magdalena (2022). A bias of Asparagine to Lysine mutations in SARS-CoV-2 outside the receptor binding domain affects protein flexibility. Frontiers in Immunology, 13 954435, 1-13. doi: 10.3389/fimmu.2022.954435 |
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2022 Journal Article A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanismParthasarathy, Shridhar, Ruggiero, Sarah McKeown, Gelot, Antoinette, Soardi, Fernanda C, Ribeiro, Bethânia F R, Pires, Douglas E V, Ascher, David B, Schmitt, Alain, Rambaud, Caroline, Represa, Alfonso, Xie, Hongbo M, Lusk, Laina, Wilmarth, Olivia, McDonnell, Pamela Pojomovsky, Juarez, Olivia A, Grace, Alexandra N, Buratti, Julien, Mignot, Cyril, Gras, Domitille, Nava, Caroline, Pierce, Samuel R, Keren, Boris, Kennedy, Benjamin C, Pena, Sergio D J, Helbig, Ingo and Cuddapah, Vishnu Anand (2022). A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanism. The American Journal of Human Genetics, 109 (12), 2253-2269. doi: 10.1016/j.ajhg.2022.11.002 |
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2022 Book Chapter Using graph-based signatures to guide rational antibody engineeringAscher, David B., Kaminskas, Lisa M., Myung, Yoochan and Pires, Douglas E. V. (2022). Using graph-based signatures to guide rational antibody engineering. Computer-aided antibody design. (pp. 375-397) New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-2609-2_21 |
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2022 Journal Article A structural biology community assessment of AlphaFold2 applicationsAkdel, Mehmet, Pires, Douglas E. V., Pardo, Eduard Porta, Jänes, Jürgen, Zalevsky, Arthur O., Mészáros, Bálint, Bryant, Patrick, Good, Lydia L., Laskowski, Roman A., Pozzati, Gabriele, Shenoy, Aditi, Zhu, Wensi, Kundrotas, Petras, Serra, Victoria Ruiz, Rodrigues, Carlos H. M., Dunham, Alistair S., Burke, David, Borkakoti, Neera, Velankar, Sameer, Frost, Adam, Basquin, Jérôme, Lindorff-Larsen, Kresten, Bateman, Alex, Kajava, Andrey V., Valencia, Alfonso, Ovchinnikov, Sergey, Durairaj, Janani, Ascher, David B., Thornton, Janet M. ... Beltrao, Pedro (2022). A structural biology community assessment of AlphaFold2 applications. Nature Structural and Molecular Biology, 29 (11), 1056-1067. doi: 10.1038/s41594-022-00849-w |
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2022 Journal Article kinCSM : Using graph‐based signatures to predict small molecule CDK2 inhibitorsZhou, Yunzhuo, Al‐Jarf, Raghad, Alavi, Azadeh, Nguyen, Thanh Binh, Rodrigues, Carlos H. M., Pires, Douglas E. V. and Ascher, David B. (2022). kinCSM : Using graph‐based signatures to predict small molecule CDK2 inhibitors. Protein Science, 31 (11) e4453, 1-11. doi: 10.1002/pro.4453 |
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2022 Journal Article cardioToxCSM: a web server for predicting cardiotoxicity of small moleculesIftkhar, Saba, de Sá, Alex G. C., Velloso, João P. L., Aljarf, Raghad, Pires, Douglas E. V. and Ascher, David B. (2022). cardioToxCSM: a web server for predicting cardiotoxicity of small molecules. Journal of Chemical Information and Modeling, 62 (20), 4827-4836. doi: 10.1021/acs.jcim.2c00822 |
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2022 Journal Article CSM‐peptides: A computational approach to rapid identification of therapeutic peptidesRodrigues, Carlos H. M., Garg, Anjali, Keizer, David, Pires, Douglas E. V. and Ascher, David B. (2022). CSM‐peptides: A computational approach to rapid identification of therapeutic peptides. Protein Science, 31 (10) e4442, 1-9. doi: 10.1002/pro.4442 |
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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 |
