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ORCIDDavid B. Ascher
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- affiliation: University of Melbourne, Bio21 Institute, Department of Biochemistry and Molecular Biology, Australia
- affiliation: Cambridge University, Department of Biochemistry, UK
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Journal Articles
- 2023
[j42]Bruna Moreira da Silva
, David B. Ascher, Douglas E. V. Pires:
epitope1D: accurate taxonomy-aware B-cell linear epitope prediction. Briefings Bioinform. 24(3) (2023)- [j41]Qisheng Pan, Stephanie Portelli, Thanh-Binh Nguyen, David B. Ascher:
Characterization on the oncogenic effect of the missense mutations of p53 via machine learning. Briefings Bioinform. 25(1) (2023) - [j40]Nathan P. Williams, Carlos H. M. Rodrigues, Jia Truong, David B. Ascher, Jessica K. Holien:
DockNet: high-throughput protein-protein interface contact prediction. Bioinform. 39(1) (2023) - [j39]Raghad Al-Jarf, Simon Tang, Douglas E. V. Pires, David B. Ascher:
embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules. J. Chem. Inf. Model. 63(2): 432-441 (2023) - [j38]Yunzhuo Zhou, Qisheng Pan, Douglas E. V. Pires, Carlos H. M. Rodrigues, David B. Ascher:
DDMut: predicting effects of mutations on protein stability using deep learning. Nucleic Acids Res. 51(W1): 122-128 (2023) - 2022
- [j37]Thanh-Binh Nguyen, Douglas E. V. Pires, David B. Ascher:
CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function. Briefings Bioinform. 23(1) (2022) - [j36]Bruna Moreira da Silva, Yoochan Myung, David B. Ascher, Douglas E. V. Pires:
epitope3D: a machine learning method for conformational B-cell epitope prediction. Briefings Bioinform. 23(1) (2022) - [j35]Qisheng Pan, Thanh-Binh Nguyen, David B. Ascher, Douglas E. V. Pires:
Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. Briefings Bioinform. 23(2) (2022) - [j34]Douglas E. V. Pires, Keith A. Stubbs, Joshua S. Mylne, David B. Ascher:
cropCSM: designing safe and potent herbicides with graph-based signatures. Briefings Bioinform. 23(2) (2022) - [j33]Pâmela M. Rezende, Joicymara S. Xavier, David B. Ascher, Gabriel R. Fernandes, Douglas E. V. Pires:
Evaluating hierarchical machine learning approaches to classify biological databases. Briefings Bioinform. 23(4) (2022) - [j32]Carlos H. M. Rodrigues, Douglas E. V. Pires, Tom L. Blundell, David B. Ascher:
Structural landscapes of PPI interfaces. Briefings Bioinform. 23(4) (2022) - [j31]Vinícius de Almeida Paiva, Murillo Ventura Mendonça, Sabrina de Azevedo Silveira, David B. Ascher, Douglas E. V. Pires, Sandro C. Izidoro:
GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms. Briefings Bioinform. 23(5) (2022) - [j30]Alex G. C. de Sá, Yangyang Long, Stephanie Portelli, Douglas E. V. Pires, David B. Ascher:
toxCSM: comprehensive prediction of small molecule toxicity profiles. Briefings Bioinform. 23(5) (2022) - [j29]Yoochan Myung, Douglas E. V. Pires, David B. Ascher:
CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function. Bioinform. 38(4): 1141-1143 (2022) - [j28]Vittoria Cicaloni, Malancha Karmakar, Luisa Frusciante, Francesco Pettini, Anna Visibelli, Maurizio Orlandini, Federico Galvagni, Maurizio Mongiat, Michael Silk, Federica Nardi, David B. Ascher, Annalisa Santucci, Ottavia Spiga:
Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93. Frontiers Bioinform. 2 (2022) - [j27]Saba Iftkhar, Alex G. C. de Sá, João P. L. Velloso, Raghad Al-Jarf, Douglas E. V. Pires, David B. Ascher:
cardioToxCSM: A Web Server for Predicting Cardiotoxicity of Small Molecules. J. Chem. Inf. Model. 62(20): 4827-4836 (2022) - [j26]Carlos H. M. Rodrigues, David B. Ascher:
CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. Nucleic Acids Res. 50(W1): 204-209 (2022) - [j25]György Abrusán, David B. Ascher, Michael Inouye:
Known allosteric proteins have central roles in genetic disease. PLoS Comput. Biol. 18(2) (2022) - 2021
- [j24]Shahid Iqbal, Fuyi Li, Tatsuya Akutsu, David B. Ascher, Geoffrey I. Webb, Jiangning Song:
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. Briefings Bioinform. 22(6) (2021) - [j23]Moi Hoon Yap, Ryo Hachiuma, Azadeh Alavi, Raphael Brüngel, Bill Cassidy, Manu Goyal, Hongtao Zhu, Johannes Rückert, Moshe Olshansky, Xiao Huang, Hideo Saito, Saeed Hassanpour, Christoph M. Friedrich, David B. Ascher, Anping Song, Hiroki Kajita, David Gillespie, Neil D. Reeves, Joseph M. Pappachan, Claire O'Shea, Eibe Frank:
Deep learning in diabetic foot ulcers detection: A comprehensive evaluation. Comput. Biol. Medicine 135: 104596 (2021) - [j22]Raghad Al-Jarf, Alex G. C. de Sá, Douglas E. V. Pires, David B. Ascher:
pdCSM-cancer: Using Graph-Based Signatures to Identify Small Molecules with Anticancer Properties. J. Chem. Inf. Model. 61(7): 3314-3322 (2021) - [j21]Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher:
pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors. J. Chem. Inf. Model. 61(11): 5438-5445 (2021) - [j20]Joicymara S. Xavier, Thanh-Binh Nguyen, Malancha Karmarkar, Stephanie Portelli, Pâmela M. Rezende, João P. L. Velloso, David B. Ascher, Douglas E. V. Pires:
ThermoMutDB: a thermodynamic database for missense mutations. Nucleic Acids Res. 49(Database-Issue): D475-D479 (2021) - [j19]Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher:
mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions. Nucleic Acids Res. 49(Webserver-Issue): 417-424 (2021) - [j18]Michael Silk, Douglas E. V. Pires, Carlos H. M. Rodrigues, Elston N. D'souza, Moshe Olshansky, Natalie Thorne, David B. Ascher:
MTR3D: identifying regions within protein tertiary structures under purifying selection. Nucleic Acids Res. 49(Webserver-Issue): 438-445 (2021) - 2020
- [j17]Yoochan Myung, Carlos H. M. Rodrigues, David B. Ascher, Douglas E. V. Pires:
mCSM-AB2: guiding rational antibody design using graph-based signatures. Bioinform. 36(5): 1453-1459 (2020) - [j16]Douglas E. V. Pires, Wandré N. P. Veloso, Yoochan Myung, Carlos H. M. Rodrigues, Michael Silk, Pâmela M. Rezende, Francislon Silva, Joicymara S. Xavier, João P. L. Velloso, Carlos Henrique da Silveira, David B. Ascher:
EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening. Bioinform. 36(14): 4200-4202 (2020) - [j15]Douglas E. V. Pires, David B. Ascher:
mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria. J. Chem. Inf. Model. 60(7): 3450-3456 (2020) - [j14]Liviu Copoiu, Pedro H. M. Torres, David B. Ascher, Tom L. Blundell, Sony Malhotra:
ProCarbDB: a database of carbohydrate-binding proteins. Nucleic Acids Res. 48(Database-Issue): D368-D375 (2020) - [j13]Yoochan Myung, Douglas E. V. Pires, David B. Ascher:
mmCSM-AB: guiding rational antibody engineering through multiple point mutations. Nucleic Acids Res. 48(Webserver-Issue): W125-W131 (2020) - [j12]Douglas E. V. Pires, Carlos H. M. Rodrigues, David B. Ascher:
mCSM-membrane: predicting the effects of mutations on transmembrane proteins. Nucleic Acids Res. 48(Webserver-Issue): W147-W153 (2020) - 2019
- [j11]Michael Silk, Slavé Petrovski, David B. Ascher:
MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Res. 47(Webserver-Issue): W121-W126 (2019) - [j10]Carlos H. M. Rodrigues, Yoochan Myung, Douglas E. V. Pires, David B. Ascher:
mCSM-PPI2: predicting the effects of mutations on protein-protein interactions. Nucleic Acids Res. 47(Webserver-Issue): W338-W344 (2019) - 2018
- [j9]Carlos H. M. Rodrigues, David B. Ascher, Douglas E. V. Pires:
Kinact: a computational approach for predicting activating missense mutations in protein kinases. Nucleic Acids Res. 46(Webserver-Issue): W127-W132 (2018) - [j8]Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher:
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. Nucleic Acids Res. 46(Webserver-Issue): W350-W355 (2018) - 2017
- [j7]Arun Prasad Pandurangan, Bernardo Ochoa-Montaño, David B. Ascher, Tom L. Blundell:
SDM: a server for predicting effects of mutations on protein stability. Nucleic Acids Res. 45(Webserver-Issue): W229-W235 (2017) - [j6]Douglas E. V. Pires, David B. Ascher:
mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions. Nucleic Acids Res. 45(Webserver-Issue): W241-W246 (2017) - 2016
- [j5]Douglas E. V. Pires, David B. Ascher:
mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures. Nucleic Acids Res. 44(Webserver-Issue): W469-W473 (2016) - [j4]Douglas E. V. Pires, David B. Ascher:
CSM-lig: a web server for assessing and comparing protein-small molecule affinities. Nucleic Acids Res. 44(Webserver-Issue): W557-W561 (2016) - 2015
- [j3]Douglas E. V. Pires, Tom L. Blundell, David B. Ascher:
Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. Nucleic Acids Res. 43(Database-Issue): 387-391 (2015) - 2014
- [j2]Douglas E. V. Pires, David B. Ascher, Tom L. Blundell:
mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinform. 30(3): 335-342 (2014) - [j1]Douglas E. V. Pires, David B. Ascher, Tom L. Blundell:
DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Res. 42(Webserver-Issue): 314-319 (2014)
Parts in Books or Collections
- 2021
- [p1]Edward Airey, Stephanie Portelli, Joicymara S. Xavier, Yoochan Myung, Michael Silk, Malancha Karmakar, João P. L. Velloso, Carlos H. M. Rodrigues, Hardik H. Parate, Anjali Garg, Raghad Al-Jarf, Lucy Barr, Juliana A. Geraldo, Pâmela M. Rezende, Douglas E. V. Pires, David B. Ascher:
Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis. Artificial Neural Networks, 3rd Edition 2021: 1-32
Informal and Other Publications
- 2023
- [i3]Bruna Moreira da Silva, David B. Ascher, Nicholas Geard, Douglas E. V. Pires:
AI driven B-cell Immunotherapy Design. CoRR abs/2309.01122 (2023) - [i2]Alex G. C. de Sá, Daniel Gould, Anna Fedyukova, Mitchell Nicholas, Lucy Dockrell, Calvin Fletcher, David Pilcher, Daniel Capurro, David B. Ascher, Khaled El-Khawas, Douglas E. V. Pires:
Explainable Machine Learning for ICU Readmission Prediction. CoRR abs/2309.13781 (2023) - 2020
- [i1]Moi Hoon Yap, Ryo Hachiuma, Azadeh Alavi, Raphael Brüngel, Manu Goyal, Hongtao Zhu, Bill Cassidy, Johannes Rückert, Moshe Olshansky, Xiao Huang, Hideo Saito, Saeed Hassanpour, Christoph M. Friedrich, David B. Ascher, Anping Song, Hiroki Kajita, David Gillespie, Neil D. Reeves, Joseph Pappachan, Claire O'Shea, Eibe Frank:
Deep Learning in Diabetic Foot Ulcers Detection: A Comprehensive Evaluation. CoRR abs/2010.03341 (2020)
Coauthor Index
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