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2021 Journal Article Assessing the performance of computational predictors for estimating protein stability changes upon missense mutationsIqbal, Shahid, Li, Fuyi, Akutsu, Tatsuya, Ascher, David B., Webb, Geoffrey I. and Song, Jiangning (2021). Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. Briefings in Bioinformatics, 22 (6) bbab184, 1-23. doi: 10.1093/bib/bbab184 |
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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 Machine Learning of ECG Waveforms to Improve Selection for Testing for Asymptomatic Left Ventricular DysfunctionPotter, Elizabeth L., Rodrigues, Carlos H. M., Ascher, David B., Abhayaratna, Walter P., Sengupta, Partho P. and Marwick, Thomas H. (2021). Machine Learning of ECG Waveforms to Improve Selection for Testing for Asymptomatic Left Ventricular Dysfunction. JACC. Cardiovascular imaging, 14 (10), 1904-1915. doi: 10.1016/j.jcmg.2021.04.020 |
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2021 Journal Article The mutation G133D on Leishmania guyanensis AQP1 is highly destabilizing as revealed by molecular modeling and hypo-osmotic shock assayTunes, Luiza G., Ascher, David B., Pires, Douglas E. V. and Monte-Neto, Rubens L. (2021). The mutation G133D on Leishmania guyanensis AQP1 is highly destabilizing as revealed by molecular modeling and hypo-osmotic shock assay. Biochimica et biophysica acta. Biomembranes, 1863 (10) 183682, 1-6. doi: 10.1016/j.bbamem.2021.183682 |
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2021 Journal Article Deep learning in diabetic foot ulcers detection: A comprehensive evaluationYap, Moi Hoon, Hachiuma, Ryo, Alavi, Azadeh, Brüngel, Raphael, Cassidy, Bill, Goyal, Manu, Zhu, Hongtao, Rückert, Johannes, Olshansky, Moshe, Huang, Xiao, Saito, Hideo, Hassanpour, Saeed, Friedrich, Christoph M., Ascher, David B., Song, Anping, Kajita, Hiroki, Gillespie, David, Reeves, Neil D., Pappachan, Joseph M., O'Shea, Claire and Frank, Eibe (2021). Deep learning in diabetic foot ulcers detection: A comprehensive evaluation. Computers in Biology and Medicine, 135 104596, 1-17. doi: 10.1016/j.compbiomed.2021.104596 |
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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 SAP domain forms a flexible part of DNA aperture in Ku70/80Hnízda, Aleš, Tesina, Petr, Nguyen, Thanh-Binh, Kukačka, Zdeněk, Kater, Lukas, Chaplin, Amanda K, Beckmann, Roland, Ascher, David B, Novák, Petr and Blundell, Tom L (2021). SAP domain forms a flexible part of DNA aperture in Ku70/80. The FEBS Journal, 288 (14), 4382-4393. doi: 10.1111/febs.15732 |
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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 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 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 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 |
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2021 Journal Article pdCSM-GPCR: predicting potent GPCR ligands with graph-based signaturesVelloso, João Paulo L., Ascher, David B. and Pires, Douglas E. V. (2021). pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures. Bioinformatics Advances, 1 (1) vbab031, vbab031. doi: 10.1093/bioadv/vbab031 |
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2020 Journal Article A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunctionHildebrand, Joanne M., Kauppi, Maria, Majewski, Ian J., Liu, Zikou, Cox, Allison J., Miyake, Sanae, Petrie, Emma J., Silk, Michael A., Li, Zhixiu, Tanzer, Maria C., Brumatti, Gabriela, Young, Samuel N., Hall, Cathrine, Garnish, Sarah E., Corbin, Jason, Stutz, Michael D., Di Rago, Ladina, Gangatirkar, Pradnya, Josefsson, Emma C., Rigbye, Kristin, Anderton, Holly, Rickard, James A., Tripaydonis, Anne, Sheridan, Julie, Scerri, Thomas S., Jackson, Victoria E., Czabotar, Peter E., Zhang, Jian-Guo, Varghese, Leila ... Silke, John (2020). A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction. Nature Communications, 11 (1) 3150, 3150. doi: 10.1038/s41467-020-16819-z |
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2020 Journal Article HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium lepraeVedithi, Sundeep Chaitanya, Malhotra, Sony, Skwark, Marcin J., Munir, Asma, Acebrón-García-De-Eulate, Marta, Waman, Vaishali P., Alsulami, Ali, Ascher, David B. and Blundell, Tom L. (2020). HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae. Computational and structural biotechnology journal, 18, 3692-3704. doi: 10.1016/j.csbj.2020.11.013 |
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2020 Journal Article The impact of size and charge on the pulmonary pharmacokinetics and immunological response of the lungs to PLGA nanoparticles after intratracheal administration to ratsHaque, Shadabul, Pouton, Colin W., McIntosh, Michelle P., Ascher, David B, Keizer, David W, Whittaker, Michael R. and Kaminskas, Lisa M. (2020). The impact of size and charge on the pulmonary pharmacokinetics and immunological response of the lungs to PLGA nanoparticles after intratracheal administration to rats. Nanomedicine: Nanotechnology, Biology, and Medicine, 30 102291, 102291. doi: 10.1016/j.nano.2020.102291 |
