David B. Ascher

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 45

Top Topics

Protein Interaction

Machine Learning

Systematic Evaluation

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

J. Chem. Inf. Model.

Publications

Alex G. C. de Sá, David B. Ascher
Towards Evolutionary-based Automated Machine Learning for Small Molecule Pharmacokinetic Prediction. GECCO Companion (2024)
Raghad Al-Jarf, Carlos H. M. Rodrigues, Yoochan Myung, Douglas E. V. Pires, David B. Ascher
piscesCSM: prediction of anticancer synergistic drug combinations. J. Cheminformatics 16 (1) (2024)
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)
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)
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 (2023)
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) (2023)
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) (2023)
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)
Bruna Moreira da Silva, David B. Ascher, Nicholas Geard, Douglas E. V. Pires
AI driven B-cell Immunotherapy Design. CoRR (2023)
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)
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)
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)
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) (2022)
György Abrusán, David B. Ascher, Michael Inouye
Known allosteric proteins have central roles in genetic disease. PLoS Comput. Biol. 18 (2) (2022)
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)
Saba Iftkhar, Alex G. C. de Sá, João P. L. Velloso, Raghad Al-Jarf, Douglas E. V. Pires, David B. Ascher
: A Web Server for Predicting Cardiotoxicity of Small Molecules. J. Chem. Inf. Model. 62 (20) (2022)
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)
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)
Carlos H. M. Rodrigues, Douglas E. V. Pires, Tom L. Blundell, David B. Ascher
Structural landscapes of PPI interfaces. Briefings Bioinform. 23 (4) (2022)
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)
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) (2022)
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)
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) (2021)
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) (2021)
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) (2021)
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)
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) (2021)
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) (2021)
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 (2021)
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) (2020)
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 (2020)
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) (2020)
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) (2020)
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) (2020)
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) (2020)
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) (2020)
Michael Silk, Slavé Petrovski, David B. Ascher
MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
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) (2019)
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) (2018)
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) (2018)
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) (2017)
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) (2017)
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) (2016)
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) (2016)
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) (2015)
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) (2014)
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) (2014)