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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 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 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 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 Understanding and predicting the functional consequences of missense mutations in BRCA1 and BRCA2Aljarf, Raghad, Shen, Mengyuan, Pires, Douglas E. V. and Ascher, David B. (2022). Understanding and predicting the functional consequences of missense mutations in BRCA1 and BRCA2. Scientific Reports, 12 (1) 10458. doi: 10.1038/s41598-022-13508-3 |
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2022 Journal Article Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93Cicaloni, Vittoria, Karmakar, Malancha, Frusciante, Luisa, Pettini, Francesco, Visibelli, Anna, Orlandini, Maurizio, Galvagni, Federico, Mongiat, Maurizio, Silk, Michael, Nardi, Federica, Ascher, David, Santucci, Annalisa and Spiga, Ottavia (2022). Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93. Frontiers in Bioinformatics, 2 891553, 1-6. doi: 10.3389/fbinf.2022.891553 |
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2022 Journal Article Germline variants in tumor suppressor FBXW7 lead to impaired ubiquitination and a neurodevelopmental syndromeStephenson, Sarah E M, Costain, Gregory, Blok, Laura E R, Silk, Michael A, Nguyen, Thanh Binh, Dong, Xiaomin, Alhuzaimi, Dana E, Dowling, James J, Walker, Susan, Amburgey, Kimberly, Hayeems, Robin Z, Rodan, Lance H, Schwartz, Marc A, Picker, Jonathan, Lynch, Sally A, Gupta, Aditi, Rasmussen, Kristen J, Schimmenti, Lisa A, Klee, Eric W, Niu, Zhiyv, Agre, Katherine E, Chilton, Ilana, Chung, Wendy K, Revah-Politi, Anya, Au, P Y Billie, Griffith, Christopher, Racobaldo, Melissa, Raas-Rothschild, Annick, Ben Zeev, Bruria ... Tan, Tiong Yang (2022). Germline variants in tumor suppressor FBXW7 lead to impaired ubiquitination and a neurodevelopmental syndrome. American Journal of Human Genetics, 109 (4), 601-617. doi: 10.1016/j.ajhg.2022.03.002 |
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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 |
