| Year |
Citation |
Score |
| 2024 |
Rodrigues CHM, Portelli S, Ascher DB. Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges. Human Genetics. PMID 38227011 DOI: 10.1007/s00439-023-02623-4 |
0.803 |
|
| 2024 |
Velloso JPL, Kovacs AS, Pires DEV, Ascher DB. AI-driven GPCR analysis, engineering, and targeting. Current Opinion in Pharmacology. 74: 102427. PMID 38219398 DOI: 10.1016/j.coph.2023.102427 |
0.799 |
|
| 2023 |
Pan Q, Portelli S, Nguyen TB, Ascher DB. Characterization on the oncogenic effect of the missense mutations of p53 via machine learning. Briefings in Bioinformatics. 25. PMID 38018912 DOI: 10.1093/bib/bbad428 |
0.809 |
|
| 2023 |
Al-Jarf R, Karmakar M, Myung Y, Ascher DB. Uncovering the Molecular Drivers of NHEJ DNA Repair-Implicated Missense Variants and Their Functional Consequences. Genes. 14. PMID 37895239 DOI: 10.3390/genes14101890 |
0.791 |
|
| 2023 |
Serghini A, Portelli S, Troadec G, Song C, Pan Q, Pires DEV, Ascher DB. Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease. Human Molecular Genetics. PMID 37883464 DOI: 10.1093/hmg/ddad181 |
0.795 |
|
| 2023 |
Rodrigues CHM, Ascher DB. CSM-Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces. Proteins. PMID 37870486 DOI: 10.1002/prot.26615 |
0.307 |
|
| 2023 |
Portelli S, Heaton R, Ascher DB. Identifying Innate Resistance Hotspots for SARS-CoV-2 Antivirals Using In Silico Protein Techniques. Genes. 14. PMID 37761839 DOI: 10.3390/genes14091699 |
0.769 |
|
| 2023 |
Ryu J, Barkal S, Yu T, Jankowiak M, Zhou Y, Francoeur M, Phan QV, Li Z, Tognon M, Brown L, Love MI, Lettre G, Ascher DB, Cassa CA, Sherwood RI, et al. Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Medrxiv : the Preprint Server For Health Sciences. PMID 37732177 DOI: 10.1101/2023.09.08.23295253 |
0.528 |
|
| 2023 |
Serghini A, Portelli S, Ascher DB. AI-Driven Enhancements in Drug Screening and Optimization. Methods in Molecular Biology (Clifton, N.J.). 2714: 269-294. PMID 37676604 DOI: 10.1007/978-1-0716-3441-7_15 |
0.733 |
|
| 2023 |
Nguyen TB, de Sá AGC, Rodrigues CHM, Pires DEV, Ascher DB. LEGO-CSM: a tool for functional characterisation of proteins. Bioinformatics (Oxford, England). PMID 37382560 DOI: 10.1093/bioinformatics/btad402 |
0.591 |
|
| 2023 |
Myung Y, Pires DEV, Ascher DB. Understanding the complementarity and plasticity of antibody-antigen interfaces. Bioinformatics (Oxford, England). 39. PMID 37382557 DOI: 10.1093/bioinformatics/btad392 |
0.716 |
|
| 2023 |
Jessen-Howard D, Pan Q, Ascher DB. Identifying the Molecular Drivers of Pathogenic Aldehyde Dehydrogenase Missense Mutations in Cancer and Non-Cancer Diseases. International Journal of Molecular Sciences. 24. PMID 37373306 DOI: 10.3390/ijms241210157 |
0.826 |
|
| 2023 |
Zhou Y, Pan Q, Pires DEV, Rodrigues CHM, Ascher DB. DDMut: predicting effects of mutations on protein stability using deep learning. Nucleic Acids Research. PMID 37283042 DOI: 10.1093/nar/gkad472 |
0.832 |
|
| 2023 |
Silk M, de Sá A, Olshansky M, Ascher DB. Insights from Spatial Measures of Intolerance to Identifying Pathogenic Variants in Developmental and Epileptic Encephalopathies. International Journal of Molecular Sciences. 24. PMID 36982187 DOI: 10.3390/ijms24065114 |
0.771 |
|
| 2022 |
Boer JC, Pan Q, Holien JK, Nguyen TB, Ascher DB, Plebanski M. A bias of Asparagine to Lysine mutations in SARS-CoV-2 outside the receptor binding domain affects protein flexibility. Frontiers in Immunology. 13: 954435. PMID 36569921 DOI: 10.3389/fimmu.2022.954435 |
0.797 |
|
| 2022 |
Xavier JS, Moir M, Tegally H, Sitharam N, Abdool Karim W, San JE, Linhares J, Wilkinson E, Ascher DB, Baxter C, Pires DEV, de Oliveira T. SARS-CoV-2 Africa dashboard for real-time COVID-19 information. Nature Microbiology. PMID 36550316 DOI: 10.1038/s41564-022-01276-9 |
0.506 |
|
| 2022 |
Cicaloni V, Karmakar M, Frusciante L, Pettini F, Visibelli A, Orlandini M, Galvagni F, Mongiat M, Silk M, Nardi F, Ascher D, Santucci A, Spiga O. Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93. Frontiers in Bioinformatics. 2: 891553. PMID 36353214 DOI: 10.3389/fbinf.2022.891553 |
0.813 |
|
| 2022 |
Ascher DB, Kaminskas LM, Myung Y, Pires DEV. Using Graph-Based Signatures to Guide Rational Antibody Engineering. Methods in Molecular Biology (Clifton, N.J.). 2552: 375-397. PMID 36346604 DOI: 10.1007/978-1-0716-2609-2_21 |
0.741 |
|
| 2022 |
Zhou Y, Al-Jarf R, Alavi A, Nguyen TB, Rodrigues CHM, Pires DEV, Ascher DB. kinCSM: Using graph-based signatures to predict small molecule CDK2 inhibitors. Protein Science : a Publication of the Protein Society. 31: e4453. PMID 36305769 DOI: 10.1002/pro.4453 |
0.782 |
|
| 2022 |
Iftkhar S, de Sá AGC, Velloso JPL, Aljarf R, Pires DEV, Ascher DB. : A Web Server for Predicting Cardiotoxicity of Small Molecules. Journal of Chemical Information and Modeling. 62: 4827-4836. PMID 36219164 DOI: 10.1021/acs.jcim.2c00822 |
0.801 |
|
| 2022 |
Portelli S, Albanaz A, Pires DEV, Ascher DB. Identifying the molecular drivers of ALS-implicated missense mutations. Journal of Medical Genetics. PMID 36180205 DOI: 10.1136/jmg-2022-108798 |
0.749 |
|
| 2022 |
Karmakar M, Cicaloni V, Rodrigues CHM, Spiga O, Santucci A, Ascher DB. 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. PMID 36118553 DOI: 10.1016/j.crstbi.2022.08.001 |
0.823 |
|
| 2022 |
Tichkule S, Myung Y, Naung MT, Ansell BRE, Guy AJ, Srivastava N, Mehra S, Cacciò SM, Mueller I, Barry AE, van Oosterhout C, Pope B, Ascher DB, Jex AR. VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses. Molecular Biology and Evolution. 39. PMID 36103257 DOI: 10.1093/molbev/msac196 |
0.758 |
|
| 2022 |
de Sá AGC, Long Y, Portelli S, Pires DEV, Ascher DB. toxCSM: comprehensive prediction of small molecule toxicity profiles. Briefings in Bioinformatics. 23. PMID 35998885 DOI: 10.1093/bib/bbac337 |
0.751 |
|
| 2022 |
Ruff KM, Choi YH, Cox D, Ormsby AR, Myung Y, Ascher DB, Radford SE, Pappu RV, Hatters DM. Sequence grammar underlying the unfolding and phase separation of globular proteins. Molecular Cell. PMID 35853451 DOI: 10.1016/j.molcel.2022.06.024 |
0.739 |
|
| 2022 |
Aljarf R, Shen M, Pires DEV, Ascher DB. Understanding and predicting the functional consequences of missense mutations in BRCA1 and BRCA2. Scientific Reports. 12: 10458. PMID 35729312 DOI: 10.1038/s41598-022-13508-3 |
0.3 |
|
| 2022 |
Rezende PM, Xavier JS, Ascher DB, Fernandes GR, Pires DEV. Evaluating hierarchical machine learning approaches to classify biological databases. Briefings in Bioinformatics. PMID 35724625 DOI: 10.1093/bib/bbac216 |
0.558 |
|
| 2022 |
Rodrigues CHM, Pires DEV, Blundell TL, Ascher DB. Structural landscapes of PPI interfaces. Briefings in Bioinformatics. PMID 35656714 DOI: 10.1093/bib/bbac165 |
0.465 |
|
| 2022 |
Stephenson SEM, Costain G, Blok LER, Silk MA, Nguyen TB, Dong X, Alhuzaimi DE, Dowling JJ, Walker S, Amburgey K, Hayeems RZ, Rodan LH, Schwartz MA, Picker J, Lynch SA, ... ... Ascher DB, et al. Germline variants in tumor suppressor FBXW7 lead to impaired ubiquitination and a neurodevelopmental syndrome. American Journal of Human Genetics. 109: 601-617. PMID 35395208 DOI: 10.1016/j.ajhg.2022.03.002 |
0.703 |
|
| 2022 |
Pan Q, Nguyen TB, Ascher DB, Pires DEV. Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. Briefings in Bioinformatics. PMID 35189634 DOI: 10.1093/bib/bbac025 |
0.829 |
|
| 2022 |
Karmakar M, Ragonnet R, Ascher DB, Trauer JM, Denholm JT. Estimating tuberculosis drug resistance amplification rates in high-burden settings. Bmc Infectious Diseases. 22: 82. PMID 35073862 DOI: 10.1186/s12879-022-07067-1 |
0.775 |
|
| 2021 |
Velloso JPL, Ascher DB, Pires DEV. pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures. Bioinformatics Advances. 1: vbab031. PMID 34901870 DOI: 10.1093/bioadv/vbab031 |
0.793 |
|
| 2021 |
Nguyen TB, Pires DEV, Ascher DB. CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function. Briefings in Bioinformatics. PMID 34882232 DOI: 10.1093/bib/bbab512 |
0.629 |
|
| 2021 |
Nguyen TB, Myung Y, de Sá AGC, Pires DEV, Ascher DB. mmCSM-NA: accurately predicting effects of single and multiple mutations on protein-nucleic acid binding affinity. Nar Genomics and Bioinformatics. 3: lqab109. PMID 34805992 DOI: 10.1093/nargab/lqab109 |
0.829 |
|
| 2021 |
Myung Y, Pires DEV, Ascher DB. CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function. Bioinformatics (Oxford, England). PMID 34734992 DOI: 10.1093/bioinformatics/btab762 |
0.732 |
|
| 2021 |
da Silva BM, Myung Y, Ascher DB, Pires DEV. epitope3D: a machine learning method for conformational B-cell epitope prediction. Briefings in Bioinformatics. PMID 34676398 DOI: 10.1093/bib/bbab423 |
0.736 |
|
| 2021 |
Zhou Y, Portelli S, Pat M, Rodrigues CHM, Nguyen TB, Pires DEV, Ascher DB. Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase. Computational and Structural Biotechnology Journal. 19: 5381-5391. PMID 34667533 DOI: 10.1016/j.csbj.2021.09.016 |
0.833 |
|
| 2021 |
Uthayopas K, de Sá AGC, Alavi A, Pires DEV, Ascher DB. TSMDA: Target and symptom-based computational model for miRNA-disease-association prediction. Molecular Therapy. Nucleic Acids. 26: 536-546. PMID 34631283 DOI: 10.1016/j.omtn.2021.08.016 |
0.756 |
|
| 2021 |
Yap MH, Hachiuma R, Alavi A, Brüngel R, Cassidy B, Goyal M, Zhu H, Rückert J, Olshansky M, Huang X, Saito H, Hassanpour S, Friedrich CM, Ascher DB, Song A, et al. Deep learning in diabetic foot ulcers detection: A comprehensive evaluation. Computers in Biology and Medicine. 135: 104596. PMID 34247133 DOI: 10.1016/j.compbiomed.2021.104596 |
0.71 |
|
| 2021 |
Zhan J, Harrison AR, Portelli S, Nguyen TB, Kojima I, Zheng S, Yan F, Masatani T, Rawlinson SM, Sethi A, Ito N, Ascher DB, Moseley GW, Gooley PR. Definition of the immune evasion-replication interface of rabies virus P protein. Plos Pathogens. 17: e1009729. PMID 34237115 DOI: 10.1371/journal.ppat.1009729 |
0.795 |
|
| 2021 |
Al-Jarf R, de Sá AGC, Pires DEV, Ascher DB. pdCSM-cancer: Using Graph-Based Signatures to Identify Small Molecules with Anticancer Properties. Journal of Chemical Information and Modeling. PMID 34213323 DOI: 10.1021/acs.jcim.1c00168 |
0.793 |
|
| 2021 |
Tunes LG, Ascher DB, Pires DV, Monte-Neto RL. 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. 183682. PMID 34175297 DOI: 10.1016/j.bbamem.2021.183682 |
0.334 |
|
| 2021 |
Portelli S, Barr L, de Sá AGC, Pires DEV, Ascher DB. Distinguishing between PTEN clinical phenotypes through mutation analysis. Computational and Structural Biotechnology Journal. 19: 3097-3109. PMID 34141133 DOI: 10.1016/j.csbj.2021.05.028 |
0.773 |
|
| 2021 |
Iqbal S, Li F, Akutsu T, Ascher DB, Webb GI, Song J. Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. Briefings in Bioinformatics. PMID 34058752 DOI: 10.1093/bib/bbab184 |
0.37 |
|
| 2021 |
Silk M, Pires DEV, Rodrigues CHM, D'Souza EN, Olshansky M, Thorne N, Ascher DB. MTR3D: identifying regions within protein tertiary structures under purifying selection. Nucleic Acids Research. PMID 34050760 DOI: 10.1093/nar/gkab428 |
0.773 |
|
| 2021 |
Rodrigues CHM, Pires DEV, Ascher DB. mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions. Nucleic Acids Research. PMID 33893812 DOI: 10.1093/nar/gkab273 |
0.371 |
|
| 2021 |
Hnízda A, Tesina P, Nguyen TB, Kukačka Z, Kater L, Chaplin A, Beckmann R, Ascher DB, Novák P, Blundell TL. SAP domain forms a flexible part of DNA aperture in Ku70/80. The Febs Journal. PMID 33511782 DOI: 10.1111/febs.15732 |
0.589 |
|
| 2021 |
Lin H, Ascher DB, Myung Y, Lamborg CH, Hallam SJ, Gionfriddo CM, Holt KE, Moreau JW. Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. The Isme Journal. PMID 33504941 DOI: 10.1038/s41396-020-00889-4 |
0.719 |
|
| 2021 |
Portelli S, Olshansky M, Rodrigues CHM, D'Souza EN, Myung Y, Silk M, Alavi A, Pires DEV, Ascher DB. Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics. PMID 33398199 DOI: 10.1038/s41588-020-00775-x |
0.762 |
|
| 2021 |
Airey E, Portelli S, Xavier JS, Myung YC, Silk M, Karmakar M, Velloso JPL, Rodrigues CHM, Parate HH, Garg A, Al-Jarf R, Barr L, Geraldo JA, Rezende PM, Pires DEV, ... Ascher DB, et al. Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis. Methods in Molecular Biology (Clifton, N.J.). 2190: 1-32. PMID 32804359 DOI: 10.1007/978-1-0716-0826-5_1 |
0.795 |
|
| 2020 |
Vedithi SC, Malhotra S, Skwark MJ, Munir A, Acebrón-García-De-Eulate M, Waman VP, Alsulami A, Ascher DB, Blundell TL. HARP: a database of structural impacts of systematic missense mutations in drug targets of . Computational and Structural Biotechnology Journal. 18: 3692-3704. PMID 33304465 DOI: 10.1016/j.csbj.2020.11.013 |
0.831 |
|
| 2020 |
Tunstall T, Portelli S, Phelan J, Clark TG, Ascher DB, Furnham N. Combining structure and genomics to understand antimicrobial resistance. Computational and Structural Biotechnology Journal. 18: 3377-3394. PMID 33294134 DOI: 10.1016/j.csbj.2020.10.017 |
0.784 |
|
| 2020 |
Xavier JS, Nguyen TB, Karmarkar M, Portelli S, Rezende PM, Velloso JPL, Ascher DB, Pires DEV. ThermoMutDB: a thermodynamic database for missense mutations. Nucleic Acids Research. PMID 33095862 DOI: 10.1093/nar/gkaa925 |
0.81 |
|
| 2020 |
Portelli S, Myung Y, Furnham N, Vedithi SC, Pires DEV, Ascher DB. Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches. Scientific Reports. 10: 18120. PMID 33093532 DOI: 10.1038/s41598-020-74648-y |
0.814 |
|
| 2020 |
Portelli S, Olshansky M, Rodrigues CHM, D'Souza EN, Myung Y, Silk M, Alavi A, Pires DEV, Ascher DB. Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics. PMID 32908256 DOI: 10.1038/s41588-020-0693-3 |
0.762 |
|
| 2020 |
Rodrigues CHM, Pires DEV, Ascher DB. DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Science : a Publication of the Protein Society. PMID 32881105 DOI: 10.1002/pro.3942 |
0.362 |
|
| 2020 |
Pires D, Ascher DB. mycoCSM: using graph-based signatures to identify safe potent hits against Mycobacteria. Journal of Chemical Information and Modeling. PMID 32615035 DOI: 10.1021/acs.jcim.0c00362 |
0.738 |
|
| 2020 |
Hildebrand JM, Kauppi M, Majewski IJ, Liu Z, Cox AJ, Miyake S, Petrie EJ, Silk MA, Li Z, Tanzer MC, Brumatti G, Young SN, Hall C, Garnish SE, Corbin J, ... ... Ascher DB, et al. A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction. Nature Communications. 11: 3150. PMID 32561755 DOI: 10.1038/S41467-020-16819-Z |
0.61 |
|
| 2020 |
Pires DEV, Rodrigues CHM, Ascher DB. mCSM-membrane: predicting the effects of mutations on transmembrane proteins. Nucleic Acids Research. PMID 32469063 DOI: 10.1093/nar/gkaa416 |
0.305 |
|
| 2020 |
Myung Y, Pires DEV, Ascher DB. mmCSM-AB: guiding rational antibody engineering through multiple point mutations. Nucleic Acids Research. PMID 32432715 DOI: 10.1093/nar/gkaa389 |
0.76 |
|
| 2020 |
Pires DEV, Veloso WNP, Myung Y, Rodrigues CHM, Silk M, Rezende PM, Silva F, Xavier JS, Velloso JPL, da Silveira CH, Ascher DB. EasyVS: a user friendly web based tool for molecule library selection and structure-based virtual screening. Bioinformatics (Oxford, England). PMID 32399551 DOI: 10.1093/bioinformatics/btaa480 |
0.773 |
|
| 2020 |
Vedithi SC, Rodrigues CHM, Portelli S, Skwark MJ, Das M, Ascher DB, Blundell TL, Malhotra S. 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. PMID 32042379 DOI: 10.1016/J.Csbj.2020.01.002 |
0.818 |
|
| 2020 |
Karmakar M, Rodrigues CHM, Horan K, Denholm JT, Ascher DB. Structure guided prediction of Pyrazinamide resistance mutations in pncA. Scientific Reports. 10: 1875. PMID 32024884 DOI: 10.1038/s41598-020-58635-x |
0.828 |
|
| 2020 |
Pires DEV, Portelli S, Rezende PM, Veloso WNP, Xavier JS, Karmakar M, Myung Y, Linhares JPV, Rodrigues CHM, Silk M, Ascher DB. A Comprehensive Computational Platform to Guide Drug Development Using Graph-Based Signature Methods. Methods in Molecular Biology (Clifton, N.J.). 2112: 91-106. PMID 32006280 DOI: 10.1007/978-1-0716-0270-6_7 |
0.79 |
|
| 2020 |
Potter EL, Rodrigues C, Ascher D, Marwick TH. MACHINE LEARNING APPLIED TO ENERGY WAVEFORM ECG FOR PREDICTION OF STAGE B HEART FAILURE IN THE COMMUNITY Journal of the American College of Cardiology. 75: 1894. DOI: 10.1016/s0735-1097(20)32521-3 |
0.7 |
|
| 2019 |
Trapero A, Pacitto A, Chan DS, Abell C, Blundell TL, Ascher DB, Coyne AG. Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH). Bioorganic & Medicinal Chemistry Letters. 126792. PMID 31757668 DOI: 10.1016/J.Bmcl.2019.126792 |
0.772 |
|
| 2019 |
Myung Y, Rodrigues CHM, Ascher DB, Pires DEV. mCSM-AB2: Guiding Rational Antibody Design Using Graph-Based Signatures. Bioinformatics (Oxford, England). PMID 31665262 DOI: 10.1093/bioinformatics/btz779 |
0.739 |
|
| 2019 |
Copoiu L, Torres PHM, Ascher DB, Blundell TL, Malhotra S. ProCarbDB: a database of carbohydrate-binding proteins. Nucleic Acids Research. PMID 31598690 DOI: 10.1093/Nar/Gkz860 |
0.751 |
|
| 2019 |
Karmakar M, Trauer JM, Ascher DB, Denholm JT. Hyper transmission of Beijing lineage Mycobacterium tuberculosis: Systematic review and Meta-analysis. The Journal of Infection. PMID 31585190 DOI: 10.1016/j.jinf.2019.09.016 |
0.755 |
|
| 2019 |
Sernee MF, Ralton JE, Nero TL, Sobala LF, Kloehn J, Vieira-Lara MA, Cobbold SA, Stanton L, Pires DEV, Hanssen E, Males A, Ward T, Bastidas LM, van der Peet PL, Parker MW, ... Ascher DB, et al. A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites. Cell Host & Microbe. 26: 385-399.e9. PMID 31513773 DOI: 10.1016/J.Chom.2019.08.009 |
0.359 |
|
| 2019 |
Silk M, Petrovski S, Ascher DB. MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Research. PMID 31170280 DOI: 10.1093/nar/gkz457 |
0.597 |
|
| 2019 |
Karmakar M, Rodrigues CHM, Holt KE, Dunstan SJ, Denholm J, Ascher DB. Empirical ways to identify novel Bedaquiline resistance mutations in AtpE. Plos One. 14: e0217169. PMID 31141524 DOI: 10.1371/journal.pone.0217169 |
0.811 |
|
| 2019 |
Rodrigues CHM, Myung Y, Pires DEV, Ascher DB. mCSM-PPI2: predicting the effects of mutations on protein-protein interactions. Nucleic Acids Research. PMID 31114883 DOI: 10.1093/nar/gkz383 |
0.79 |
|
| 2019 |
Singh V, Pacitto A, Donini S, Ferraris DM, Boros S, Illyés E, Szokol B, Rizzi M, Blundell TL, Ascher DB, Pato J, Mizrahi V. Synthesis and Structure-Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH. European Journal of Medicinal Chemistry. 174: 309-329. PMID 31055147 DOI: 10.1016/j.ejmech.2019.04.027 |
0.785 |
|
| 2019 |
Pires DEV, Rodrigues CHM, Albanaz ATS, Karmakar M, Myung Y, Xavier J, Michanetzi EM, Portelli S, Ascher DB. Exploring Protein Supersecondary Structure Through Changes in Protein Folding, Stability, and Flexibility. Methods in Molecular Biology (Clifton, N.J.). 1958: 173-185. PMID 30945219 DOI: 10.1007/978-1-4939-9161-7_9 |
0.822 |
|
| 2018 |
Portelli S, Phelan JE, Ascher DB, Clark TG, Furnham N. Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. Scientific Reports. 8: 15356. PMID 30337649 DOI: 10.1038/S41598-018-33370-6 |
0.78 |
|
| 2018 |
Vedithi SC, Malhotra S, Das M, Daniel S, Kishore N, George A, Arumugam S, Rajan L, Ebenezer M, Ascher DB, Arnold E, Blundell TL. Publisher Correction: Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae. Scientific Reports. 8: 8250. PMID 29789675 DOI: 10.1038/S41598-018-26451-Z |
0.792 |
|
| 2018 |
Rodrigues CHM, Ascher DB, Pires DEV. Kinact: a computational approach for predicting activating missense mutations in protein kinases. Nucleic Acids Research. PMID 29788456 DOI: 10.1093/nar/gky375 |
0.357 |
|
| 2018 |
Rodrigues CHM, Pires DEV, Ascher DB. DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. Nucleic Acids Research. PMID 29718330 DOI: 10.1093/nar/gky300 |
0.332 |
|
| 2018 |
Karmakar M, Globan M, Fyfe JAM, Stinear TP, Johnson PDR, Holmes NE, Denholm JT, Ascher DB. Analysis of a Novel pncA Mutation for Susceptibility to Pyrazinamide Therapy. American Journal of Respiratory and Critical Care Medicine. PMID 29694240 DOI: 10.1164/rccm.201712-2572LE |
0.794 |
|
| 2018 |
Vedithi SC, Malhotra S, Das M, Daniel S, Kishore N, George A, Arumugam S, Rajan L, Ebenezer M, Ascher DB, Arnold E, Blundell TL. Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae. Scientific Reports. 8: 5016. PMID 29567948 DOI: 10.1038/S41598-018-23423-1 |
0.816 |
|
| 2018 |
Trapero A, Pacitto A, Singh V, Sabbah M, Coyne AG, Mizrahi V, Blundell TL, Ascher DB, Abell C. A fragment-based approach to targeting inosine-5´-monophosphate dehydrogenase (IMPDH) from Mycobacterium tuberculosis. Journal of Medicinal Chemistry. PMID 29547284 DOI: 10.1021/Acs.Jmedchem.7B01622 |
0.792 |
|
| 2018 |
Hnízda A, Fábry M, Moriyama T, Pachl P, Kugler M, Brinsa V, Ascher DB, Carroll WL, Novák P, Žaliová M, Trka J, Řezáčová P, Yang JJ, Veverka V. Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation. Leukemia. PMID 29535428 DOI: 10.1038/s41375-018-0073-5 |
0.336 |
|
| 2017 |
Traynelis J, Silk M, Wang Q, Berkovic SF, Liu L, Ascher DB, Balding DJ, Petrovski S. Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation. Genome Research. PMID 28864458 DOI: 10.1101/gr.226589.117 |
0.599 |
|
| 2017 |
Chirgadze DY, Ascher DB, Blundell TL, Sibanda BL. DNA-PKcs, Allostery, and DNA Double-Strand Break Repair: Defining the Structure and Setting the Stage. Methods in Enzymology. 592: 145-157. PMID 28668119 DOI: 10.1016/bs.mie.2017.04.001 |
0.381 |
|
| 2017 |
Pandurangan AP, Ochoa-Montaño B, Ascher DB, Blundell TL. SDM: a server for predicting effects of mutations on protein stability. Nucleic Acids Research. PMID 28525590 DOI: 10.1093/nar/gkx439 |
0.81 |
|
| 2017 |
Albanaz ATS, Rodrigues CHM, Pires DEV, Ascher DB. Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design. Expert Opinion On Drug Discovery. 12: 553-563. PMID 28490289 DOI: 10.1080/17460441.2017.1322579 |
0.4 |
|
| 2017 |
Pandurangan AP, Ascher DB, Thomas SE, Blundell TL. Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance. Biochemical Society Transactions. 45: 303-311. PMID 28408471 DOI: 10.1042/BST20160422 |
0.813 |
|
| 2017 |
Pires DE, Ascher DB. mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions. Nucleic Acids Research. PMID 28383703 DOI: 10.1093/nar/gkx236 |
0.788 |
|
| 2017 |
Sibanda BL, Chirgadze DY, Ascher DB, Blundell TL. DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair. Science (New York, N.Y.). 355: 520-524. PMID 28154079 DOI: 10.1126/science.aak9654 |
0.392 |
|
| 2016 |
Jubb HC, Higueruelo AP, Ochoa-Montaño B, Pitt WR, Ascher DB, Blundell TL. Arpeggio: A web server for calculating and visualising interatomic interactions in protein structures. Journal of Molecular Biology. PMID 27964945 DOI: 10.1016/j.jmb.2016.12.004 |
0.796 |
|
| 2016 |
Kano FS, Souza-Silva FA, Torres LM, Lima BA, Sousa TN, Alves JR, Rocha RS, Fontes CJ, Sanchez BA, Adams JH, Brito CF, Pires DE, Ascher DB, Sell AM, Carvalho LH. The Presence, Persistence and Functional Properties of Plasmodium vivax Duffy Binding Protein II Antibodies Are Influenced by HLA Class II Allelic Variants. Plos Neglected Tropical Diseases. 10: e0005177. PMID 27959918 DOI: 10.1371/Journal.Pntd.0005177 |
0.711 |
|
| 2016 |
Jubb HC, Pandurangan AP, Turner MA, Ochoa-Montaño B, Blundell TL, Ascher DB. Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health. Progress in Biophysics and Molecular Biology. PMID 27913149 DOI: 10.1016/j.pbiomolbio.2016.10.002 |
0.835 |
|
| 2016 |
Parker LJ, Bocedi A, Ascher DB, Aitken JB, Harris HH, Lo Bello M, Ricci G, Morton CJ, Parker MW. Glutathione transferase P1-1 as an arsenic drug-sequestering enzyme. Protein Science : a Publication of the Protein Society. PMID 27863446 DOI: 10.1002/pro.3084 |
0.404 |
|
| 2016 |
Singh V, Donini S, Pacitto A, Sala C, Hartkoorn RC, Dhar N, Keri G, Ascher DB, Mondésert G, Vocat A, Lupien A, Sommer R, Vermet H, Lagrange S, Buechler J, et al. The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis. Acs Infectious Diseases. PMID 27726334 DOI: 10.1021/Acsinfecdis.6B00102 |
0.806 |
|
| 2016 |
Park Y, Pacitto A, Bayliss T, Cleghorn LA, Wang Z, Hartman T, Arora K, Ioerger TR, Sacchettini J, Rizzi M, Donini S, Blundell TL, Ascher DB, Rhee KY, Breda A, et al. Essential but not vulnerable: indazole sulfonamides targeting inosine monophosphate dehydrogenase as potential leads against Mycobacterium tuberculosis. Acs Infectious Diseases. PMID 27704782 DOI: 10.1021/Acsinfecdis.6B00103 |
0.794 |
|
| 2016 |
Coelho MB, Ascher DB, Gooding C, Lang E, Maude H, Turner D, Llorian M, Pires DE, Attig J, Smith CW. Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins. Biochemical Society Transactions. 44: 1058-65. PMID 27528752 DOI: 10.1042/BST20160080 |
0.721 |
|
| 2016 |
Silvino AC, Costa GL, Araújo FC, Ascher DB, Pires DE, Fontes CJ, Carvalho LH, Brito CF, Sousa TN. Variation in Human Cytochrome P-450 Drug-Metabolism Genes: A Gateway to the Understanding of Plasmodium vivax Relapses. Plos One. 11: e0160172. PMID 27467145 DOI: 10.1371/journal.pone.0160172 |
0.735 |
|
| 2016 |
Pires DE, Blundell TL, Ascher DB. mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance. Scientific Reports. 6: 29575. PMID 27384129 DOI: 10.1038/srep29575 |
0.827 |
|
| 2016 |
Pires DE, Ascher DB. mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures. Nucleic Acids Research. PMID 27216816 DOI: 10.1093/nar/gkw458 |
0.748 |
|
| 2016 |
Pires DE, Ascher DB. CSM-lig: a web server for assessing and comparing protein-small molecule affinities. Nucleic Acids Research. PMID 27151202 DOI: 10.1093/nar/gkw390 |
0.772 |
|
| 2016 |
Phelan J, Coll F, McNerney R, Ascher DB, Pires DE, Furnham N, Coeck N, Hill-Cawthorne GA, Nair MB, Mallard K, Ramsay A, Campino S, Hibberd ML, Pain A, Rigouts L, et al. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. Bmc Medicine. 14: 31. PMID 27005572 DOI: 10.1186/S12916-016-0575-9 |
0.789 |
|
| 2016 |
Pires DE, Chen J, Blundell TL, Ascher DB. In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. Scientific Reports. 6: 19848. PMID 26797105 DOI: 10.1038/srep19848 |
0.82 |
|
| 2016 |
Liang S, Esswein SR, Ochi T, Wu Q, Ascher DB, Chirgadze D, Sibanda BL, Blundell TL. Achieving selectivity in space and time with DNA double-strand-break response and repair: molecular stages and scaffolds come with strings attached Structural Chemistry. 28: 161-171. DOI: 10.1007/S11224-016-0841-7 |
0.638 |
|
| 2015 |
Pacitto A, Ascher DB, Wong LH, Blaszczyk BK, Nookala RK, Zhang N, Dokudovskaya S, Levine TP, Blundell TL. Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein. Open Biology. 5. PMID 26631379 DOI: 10.1098/rsob.150174 |
0.777 |
|
| 2015 |
Blaszczyk M, Harmer NJ, Chirgadze DY, Ascher DB, Blundell TL. Achieving high signal-to-noise in cell regulatory systems: Spatial organization of multiprotein transmembrane assemblies of FGFR and MET receptors. Progress in Biophysics and Molecular Biology. PMID 25957048 DOI: 10.1016/j.pbiomolbio.2015.04.007 |
0.651 |
|
| 2015 |
Jafri M, Wake NC, Ascher DB, Pires DE, Gentle D, Morris MR, Rattenberry E, Simpson MA, Trembath RC, Weber A, Woodward ER, Donaldson A, Blundell TL, Latif F, Maher ER. Germline Mutations in the CDKN2B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma. Cancer Discovery. 5: 723-9. PMID 25873077 DOI: 10.1158/2159-8290.CD-14-1096 |
0.778 |
|
| 2015 |
Pires DE, Blundell TL, Ascher DB. pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. Journal of Medicinal Chemistry. 58: 4066-72. PMID 25860834 DOI: 10.1021/acs.jmedchem.5b00104 |
0.767 |
|
| 2015 |
Nemethova M, Radvanszky J, Kadasi L, Ascher DB, Pires DE, Blundell TL, Porfirio B, Mannoni A, Santucci A, Milucci L, Sestini S, Biolcati G, Sorge F, Aurizi C, Aquaron R, et al. Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on 'black bone disease' in Italy. European Journal of Human Genetics : Ejhg. PMID 25804398 DOI: 10.1038/Ejhg.2015.60 |
0.742 |
|
| 2015 |
Usher JL, Ascher DB, Pires DE, Milan AM, Blundell TL, Ranganath LR. Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations. Jimd Reports. PMID 25681086 DOI: 10.1007/8904_2014_380 |
0.797 |
|
| 2015 |
Jubb H, Blundell TL, Ascher DB. Flexibility and small pockets at protein-protein interfaces: New insights into druggability. Progress in Biophysics and Molecular Biology. PMID 25662442 DOI: 10.1016/j.pbiomolbio.2015.01.009 |
0.803 |
|
| 2015 |
Hermans SJ, Ascher DB, Hancock NC, Holien JK, Michell BJ, Chai SY, Morton CJ, Parker MW. Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides. Protein Science : a Publication of the Protein Society. 24: 190-9. PMID 25408552 DOI: 10.1002/pro.2604 |
0.379 |
|
| 2015 |
Pires DE, Blundell TL, Ascher DB. Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. Nucleic Acids Research. 43: D387-91. PMID 25324307 DOI: 10.1093/nar/gku966 |
0.813 |
|
| 2015 |
Ascher DB, Jubb HC, Pires DEV, Ochi T, Higueruelo A, Blundell TL. Protein-protein interactions: Structures and druggability Nato Science For Peace and Security Series a: Chemistry and Biology. 38: 141-163. DOI: 10.1007/978-94-017-9719-1_12 |
0.791 |
|
| 2015 |
Hermans SJ, Ascher DB, Hancock NC, Holien JK, Michell BJ, Chai SY, Morton CJ, Parker MW. Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides Protein Science. 24: 190-199. DOI: 10.1002/pro.2604 |
0.325 |
|
| 2014 |
Watt AD, Crespi GA, Down RA, Ascher DB, Gunn A, Perez KA, McLean CA, Villemagne VL, Parker MW, Barnham KJ, Miles LA. Anti-Aβ antibody target engagement: a response to Siemers et al. Acta Neuropathologica. 128: 611-4. PMID 25120193 DOI: 10.1007/S00401-014-1333-8 |
0.308 |
|
| 2014 |
Pires DE, Ascher DB, Blundell TL. DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Research. 42: W314-9. PMID 24829462 DOI: 10.1093/nar/gku411 |
0.8 |
|
| 2014 |
Watt AD, Crespi GA, Down RA, Ascher DB, Gunn A, Perez KA, McLean CA, Villemagne VL, Parker MW, Barnham KJ, Miles LA. Do current therapeutic anti-Aβ antibodies for Alzheimer's disease engage the target? Acta Neuropathologica. 127: 803-10. PMID 24803227 DOI: 10.1007/S00401-014-1290-2 |
0.359 |
|
| 2014 |
Ascher DB, Wielens J, Nero TL, Doughty L, Morton CJ, Parker MW. Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA Scientific Reports. 4. PMID 24755925 DOI: 10.1038/srep04765 |
0.402 |
|
| 2014 |
Crespi GA, Ascher DB, Parker MW, Miles LA. Crystallization and preliminary X-ray diffraction analysis of the Fab portion of the Alzheimer's disease immunotherapy candidate bapineuzumab complexed with amyloid-β. Acta Crystallographica. Section F, Structural Biology Communications. 70: 374-7. PMID 24598931 DOI: 10.1107/S2053230X14001642 |
0.335 |
|
| 2014 |
Feil SC, Ascher DB, Kuiper MJ, Tweten RK, Parker MW. Structural studies of Streptococcus pyogenes streptolysin O provide insights into the early steps of membrane penetration. Journal of Molecular Biology. 426: 785-92. PMID 24316049 DOI: 10.1016/J.Jmb.2013.11.020 |
0.378 |
|
| 2014 |
Pires DE, Ascher DB, Blundell TL. mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics (Oxford, England). 30: 335-42. PMID 24281696 DOI: 10.1093/bioinformatics/btt691 |
0.815 |
|
| 2012 |
Ascher DB, Polekhina G, Parker MW. Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 68: 468-71. PMID 22505422 DOI: 10.1107/S1744309112006963 |
0.38 |
|
| 2012 |
Parker LJ, Ascher DB, Gao C, Miles LA, Harris HH, Parker MW. Structural approaches to probing metal interaction with proteins. Journal of Inorganic Biochemistry. 115: 138-47. PMID 22437159 DOI: 10.1016/j.jinorgbio.2012.02.015 |
0.445 |
|
| 2011 |
Parker LJ, Italiano LC, Morton CJ, Hancock NC, Ascher DB, Aitken JB, Harris HH, Campomanes P, Rothlisberger U, De Luca A, Lo Bello M, Ang WH, Dyson PJ, Parker MW. Studies of glutathione transferase P1-1 bound to a platinum(IV)-based anticancer compound reveal the molecular basis of its activation Chemistry - a European Journal. 17: 7806-7816. PMID 21681839 DOI: 10.1002/chem.201100586 |
0.443 |
|
| 2011 |
Ascher DB, Cromer BA, Morton CJ, Volitakis I, Cherny RA, Albiston AL, Chai SY, Parker MW. Regulation of insulin-regulated membrane aminopeptidase activity by its C-terminal domain Biochemistry. 50: 2611-2622. PMID 21348480 DOI: 10.1021/bi101893w |
0.409 |
|
| 2011 |
Parker LJ, Italiano LC, Morton CJ, Hancock NC, Ascher DB, Aitken JB, Harris HH, Campomanes P, Rothlisberger U, De Luca A, Lo Bello M, Ang WH, Dyson PJ, Parker MW. Cover Picture: Studies of Glutathione Transferase P1‐1 Bound to a Platinum(IV)‐Based Anticancer Compound Reveal the Molecular Basis of Its Activation (Chem. Eur. J. 28/2011) Chemistry – a European Journal. 17: 7705-7705. DOI: 10.1002/CHEM.201190140 |
0.356 |
|
| 2008 |
Chai SY, Yeatman HR, Parker MW, Ascher DB, Thompson PE, Mulvey HT, Albiston AL. Development of cognitive enhancers based on inhibition of insulin-regulated aminopeptidase. Bmc Neuroscience. 9: S14. PMID 19090987 DOI: 10.1186/1471-2202-9-S2-S14 |
0.322 |
|
| 2008 |
Albiston AL, Morton CJ, Ng HL, Pham V, Yeatman HR, Ye S, Fernando RN, De Bundel D, Ascher DB, Mendelsohn FA, Parker MW, Chai SY. Identification and characterization of a new cognitive enhancer based on inhibition of insulin-regulated aminopeptidase. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 22: 4209-17. PMID 18716029 DOI: 10.1096/fj.08-112227 |
0.367 |
|
| 2008 |
Ye S, Chai SY, Lew RA, Ascher DB, Morton CJ, Parker MW, Albiston AL. Identification of modulating residues defining the catalytic cleft of insulin-regulated aminopeptidase Biochemistry and Cell Biology. 86: 251-261. PMID 18523486 DOI: 10.1139/O08-037 |
0.393 |
|
| 2008 |
Wun KS, Miles LA, Crespi GA, Wycherley K, Ascher DB, Barnham KJ, Cappai R, Beyreuther K, Masters CL, Parker MW, McKinstry WJ. Crystallization and preliminary X-ray diffraction analysis of the Fab fragment of WO2, an antibody specific for the Abeta peptides associated with Alzheimer's disease. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 64: 438-41. PMID 18453721 DOI: 10.1107/S1744309108011718 |
0.334 |
|
| 2008 |
Ascher DB, Crespi GAN, Ng HL, Morton CJ, Parker MW, Miles LA. Novel Therapeutic Approaches to Treat Alzheimer’s Disease and Memory Disorders Journal of Proteomics & Bioinformatics. 1: 464-476. DOI: 10.4172/JPB.1000054 |
0.335 |
|
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