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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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2021 Book Chapter Identifying genotype-phenotype correlations via integrative mutation analysisAirey, Edward, Portelli, Stephanie, Xavier, Joicymara S, Myung, Yoo Chan, Silk, Michael, Karmakar, Malancha, Velloso, João P L, Rodrigues, Carlos H M, Parate, Hardik H, Garg, Anjali, Al-Jarf, Raghad, Barr, Lucy, Geraldo, Juliana A, Rezende, Pâmela M, Pires, Douglas E V and Ascher, David B (2021). Identifying genotype-phenotype correlations via integrative mutation analysis. Artificial neural networks. (pp. 1-32) edited by Hugh Cartwright. New York, NY, United States: Humana. doi: 10.1007/978-1-0716-0826-5_1 |
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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 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 |
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2020 Journal Article ThermoMutDB: a thermodynamic database for missense mutationsXavier, Joicymara S, Nguyen, Thanh-Binh, Karmarkar, Malancha, Portelli, Stephanie, Rezende, Pâmela M, Velloso, João P L, Ascher, David B and Pires, Douglas E V (2020). ThermoMutDB: a thermodynamic database for missense mutations. Nucleic Acids Research, 49 (D1), D475-D479. doi: 10.1093/nar/gkaa925 |
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2020 Journal Article Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approachesPortelli, Stephanie, Myung, Yoochan, Furnham, Nicholas, Vedithi, Sundeep Chaitanya, Pires, Douglas E. V. and Ascher, David B. (2020). Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches. Scientific Reports, 10 (1) 18120, 1-13. doi: 10.1038/s41598-020-74648-y |
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2020 Journal Article DynaMut2 : Assessing changes in stability and flexibility upon single and multiple point missense mutationsRodrigues, Carlos H.M., Pires, Douglas E.V. and Ascher, David B. (2020). DynaMut2 : Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Science, 30 (1), 60-69. doi: 10.1002/pro.3942 |
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2020 Journal Article 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. (2020). Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 52 (10), 999-1001. doi: 10.1038/s41588-020-0693-3 |
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2020 Journal Article EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screeningPires, Douglas E V, Veloso, Wandré N P, Myung, YooChan, Rodrigues, Carlos H M, Silk, Michael, Rezende, Pâmela M, Silva, Francislon, Xavier, Joicymara S, Velloso, João P L, da Silveira, Carlos H and Ascher, David B (2020). EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening. Bioinformatics, 36 (14), 4200-4202. doi: 10.1093/bioinformatics/btaa480 |
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2020 Journal Article mycoCSM: Using graph-based signatures to identify safe potent hits against MycobacteriaPires, Douglas E. V. and Ascher, David B. (2020). mycoCSM: Using graph-based signatures to identify safe potent hits against Mycobacteria. Journal of Chemical Information and Modeling, 60 (7), 3450-3456. doi: 10.1021/acs.jcim.0c00362 |
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2020 Journal Article mCSM-membrane: predicting the effects of mutations on transmembrane proteinsPires, Douglas E V, Rodrigues, Carlos H M and Ascher, David B (2020). mCSM-membrane: predicting the effects of mutations on transmembrane proteins. Nucleic Acids Research, 48 (W1), W147-W153. doi: 10.1093/nar/gkaa416 |
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2020 Journal Article mmCSM-AB: guiding rational antibody engineering through multiple point mutationsMyung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2020). mmCSM-AB: guiding rational antibody engineering through multiple point mutations. Nucleic Acids Research, 48 (W1), W125-W131. doi: 10.1093/nar/gkaa389 |
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2020 Journal Article mCSM-AB2: guiding rational antibody design using graph-based signaturesMyung, Yoochan, Rodrigues, Carlos H. M., Ascher, David B. and Pires, Douglas E. V. (2020). mCSM-AB2: guiding rational antibody design using graph-based signatures. Bioinformatics, 36 (5), 1453-1459. doi: 10.1093/bioinformatics/btz779 |
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2020 Journal Article Structure guided prediction of Pyrazinamide resistance mutations in pncAKarmakar, Malancha, Rodrigues, Carlos H. M., Horan, Kristy, Denholm, Justin T. and Ascher, David B. (2020). Structure guided prediction of Pyrazinamide resistance mutations in pncA. Scientific Reports, 10 (1) 1875, 1875. doi: 10.1038/s41598-020-58635-x |
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2020 Journal Article Widespread remodeling of proteome solubility in response to different protein homeostasis stressesSui, Xiaojing, Pires, Douglas E V, Ormsby, Angelique R, Cox, Dezerae, Nie, Shuai, Vecchi, Giulia, Vendruscolo, Michele, Ascher, David B, Reid, Gavin E and Hatters, Danny M (2020). Widespread remodeling of proteome solubility in response to different protein homeostasis stresses. Proceedings of the National Academy of Sciences of the United States of America, 117 (5), 2422-2431. doi: 10.1073/pnas.1912897117 |
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2020 Journal Article Variant type is associated with disease characteristics in SDHB, SDHC and SDHD-linked phaeochromocytoma-paragangliomaBayley, Jean Pierre, Bausch, Birke, Rijken, Johannes Adriaan, van Hulsteijn, Leonie Theresia, Jansen, Jeroen C., Ascher, David, Pires, Douglas Eduardo Valente, Hes, Frederik J., Hensen, Erik F., Corssmit, Eleonora P. M., Devilee, Peter and Neumann, Hartmut P. H. (2020). Variant type is associated with disease characteristics in SDHB, SDHC and SDHD-linked phaeochromocytoma-paraganglioma. Journal of Medical Genetics, 57 (2), 96-103. doi: 10.1136/jmedgenet-2019-106214 |
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2020 Journal Article Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase inVedithi, Sundeep Chaitanya, Rodrigues, Carlos H. M., Portelli, Stephanie, Skwark, Marcin J., Das, Madhusmita, Ascher, David B., Blundell, Tom L. and Malhotra, Sony (2020). Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in . Computational and Structural Biotechnology Journal, 18, 271-286. doi: 10.1016/j.csbj.2020.01.002 |
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2020 Journal Article Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH)Trapero, Ana, Pacitto, Angela, Chan, Daniel Shiu-Hin, Abell, Chris, Blundell, Tom L., Ascher, David B. and Coyne, Anthony G. (2020). Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH). Bioorganic and Medicinal Chemistry Letters, 30 (2) 126792, 126792. doi: 10.1016/j.bmcl.2019.126792 |
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2020 Book Chapter A comprehensive computational platform to guide drug development using graph-based signature methodsPires, Douglas E. V., Portelli, Stephanie, Rezende, Pâmela M., Veloso, Wandré N. P., Xavier, Joicymara S., Karmakar, Malancha, Myung, Yoochan, Linhares, João P. V., Rodrigues, Carlos H. M., Silk, Michael and Ascher, David B. (2020). A comprehensive computational platform to guide drug development using graph-based signature methods. Structural bioinformatics: methods and protocols. (pp. 91-106) New York, NY, United States: Humana. doi: 10.1007/978-1-0716-0270-6_7 |
