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2024 Journal Article A broad-spectrum α-glucosidase of glycoside hydrolase family 13 from Marinovum sp., a member of the Roseobacter cladeLi, Jinling, Mui, Janice W.-Y., da Silva, Bruna M., Pires, Douglas E.V., Ascher, David B., Madiedo Soler, Niccolay, Goddard-Borger, Ethan D. and Williams, Spencer J. (2024). A broad-spectrum α-glucosidase of glycoside hydrolase family 13 from Marinovum sp., a member of the Roseobacter clade. Applied Biochemistry and Biotechnology, 196 (9), 6059-6071. doi: 10.1007/s12010-023-04820-3 |
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2024 Journal Article Characterization on the oncogenic effect of the missense mutations of p53 via machine learningPan, Qisheng, Portelli, Stephanie, Nguyen, Thanh Binh and Ascher, David B. (2024). Characterization on the oncogenic effect of the missense mutations of p53 via machine learning. Briefings in Bioinformatics, 25 (1) bbad428, 1-13. doi: 10.1093/bib/bbad428 |
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2024 Book Chapter AI-driven enhancements in drug screening and optimizationSerghini, Adam, Portelli, Stephanie and Ascher, David B. (2024). AI-driven enhancements in drug screening and optimization. Computational drug discovery and design. (pp. 269-294) edited by Mohini Gore and Umesh B. Jagtap. New York, NY, United States: Humana. doi: 10.1007/978-1-0716-3441-7_15 |
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2024 Journal Article Lipid sulfoxide polymers as potential inhalable drug delivery platforms with differential albumin binding affinityEdiriweera, Gayathri R., Butcher, Neville J., Kothapalli, Ashok, Zhao, Jiacheng, Blanchfield, Joanne T., Subasic, Christopher N., Grace, James L., Fu, Changkui, Tan, Xiao, Quinn, John F., Ascher, David B., Whittaker, Michael R., Whittaker, Andrew K. and Kaminskas, Lisa M. (2024). Lipid sulfoxide polymers as potential inhalable drug delivery platforms with differential albumin binding affinity. Biomaterials Science, 12 (11), 2978-2992. doi: 10.1039/d3bm02020g |
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2023 Journal Article Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau diseaseSerghini, Adam, Portelli, Stephanie, Troadec, Guillaume, Song, Catherine, Pan, Qisheng, Pires, Douglas E. V. and Ascher, David B. (2023). Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease. Human Molecular Genetics, 33 (3), 224-232. doi: 10.1093/hmg/ddad181 |
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2023 Journal Article CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfacesRodrigues, Carlos H. M. and Ascher, David B. (2023). CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces. Proteins: Structure, Function, and Bioinformatics, 93 (1), 209-216. doi: 10.1002/prot.26615 |
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2023 Journal Article Uncovering the molecular drivers of NHEJ DNA repair-implicated missense variants and their functional consequencesAl-Jarf, Raghad, Karmakar, Malancha, Myung, Yoochan and Ascher, David B. (2023). Uncovering the molecular drivers of NHEJ DNA repair-implicated missense variants and their functional consequences. Genes, 14 (10) 1890, 1-11. doi: 10.3390/genes14101890 |
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2023 Journal Article Identifying innate resistance hotspots for SARS-CoV-2 antivirals using in silico protein techniquesPortelli, Stephanie, Heaton, Ruby and Ascher, David B. (2023). Identifying innate resistance hotspots for SARS-CoV-2 antivirals using in silico protein techniques. Genes, 14 (9) 1699, 1-13. doi: 10.3390/genes14091699 |
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2023 Journal Article Understanding the complementarity and plasticity of antibody–antigen interfacesMyung, Yoochan, Pires, Douglas E. V. and Ascher, David B (2023). Understanding the complementarity and plasticity of antibody–antigen interfaces. Bioinformatics, 39 (7) btad392, 1-7. doi: 10.1093/bioinformatics/btad392 |
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2023 Journal Article LEGO-CSM: a tool for functional characterization of proteinsNguyen, Thanh Binh, de Sá, Alex G. C., Rodrigues, Carlos H. M., Pires, Douglas E. V. and Ascher, David B. (2023). LEGO-CSM: a tool for functional characterization of proteins. Bioinformatics, 39 (7) btad402, 1-4. doi: 10.1093/bioinformatics/btad402 |
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2023 Journal Article Identifying the molecular drivers of pathogenic aldehyde dehydrogenase missense mutations in cancer and non-cancer diseasesJessen-Howard, Dana, Pan, Qisheng and Ascher, David B. (2023). Identifying the molecular drivers of pathogenic aldehyde dehydrogenase missense mutations in cancer and non-cancer diseases. International Journal of Molecular Sciences, 24 (12) 10157, 1-18. doi: 10.3390/ijms241210157 |
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2023 Journal Article DDMut: predicting effects of mutations on protein stability using deep learningZhou, Yunzhuo, Pan, Qisheng, Pires, Douglas E. V., Rodrigues, Carlos H. M. and Ascher, David B. (2023). DDMut: predicting effects of mutations on protein stability using deep learning. Nucleic Acids Research, 51 (W1), W122-W128. doi: 10.1093/nar/gkad472 |
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2023 Journal Article epitope1D: accurate taxonomy-aware B-cell linear epitope predictionda Silva, Bruna Moreira, Ascher, David B. and Pires, Douglas E. V. (2023). epitope1D: accurate taxonomy-aware B-cell linear epitope prediction. Briefings in Bioinformatics, 24 (3) bbad114, 1-8. doi: 10.1093/bib/bbad114 |
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2023 Journal Article Insights from spatial measures of intolerance to identifying pathogenic variants in developmental and epileptic encephalopathiesSilk, Michael, de Sá, Alex, Olshansky, Moshe and Ascher, David B. (2023). Insights from spatial measures of intolerance to identifying pathogenic variants in developmental and epileptic encephalopathies. International Journal of Molecular Sciences, 24 (6) 5114, 1-9. doi: 10.3390/ijms24065114 |
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2023 Journal Article CSM-Toxin: a web-server for predicting protein toxicityMorozov, Vladimir, Rodrigues, Carlos H. M. and Ascher, David B. (2023). CSM-Toxin: a web-server for predicting protein toxicity. Pharmaceutics, 15 (2) 431, 1-8. doi: 10.3390/pharmaceutics15020431 |
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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 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 (2023). 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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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 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 |
