David B. Ascher

57 papers Journal 54Unranked 2
YearRankTypeTitle / Venue / Authors
2026 J jnl
An Empirical Analysis of Fine-Tuning Large Language Models on Bioinformatics Literature: PRSGPT and BioStarsGPT.
CoRR
Muhammad Muneeb, David B. Ascher
2026 J jnl
DPD-Cancer: Explainable Graph-based Deep Learning for Small Molecule Anti-Cancer Activity Prediction.
CoRR
Magnus H. Strømme, Alex G. C. de Sá, David B. Ascher
2026 J jnl
G2DR: A Genotype-First Framework for Genetics-Informed Target Prioritization and Drug Repurposing.
CoRR
Muhammad Muneeb, David B. Ascher
2026 J jnl
kinCSM-RTK: Machine Learning-Based Screening of Receptor Tyrosine Kinase Inhibitors in Drug Discovery.
J. Chem. Inf. Model.
Adam Serghini, Yunzhuo Zhou, Yoochan Myung, Alex G. C. de Sá, Stephanie Portelli, David B. Ascher
2025 J jnl
Auto-ADMET: An Effective and Interpretable AutoML Method for Chemical ADMET Property Prediction.
CoRR
Alex G. C. de Sá, David B. Ascher
2025 J jnl
Comparative Analysis of 47 Context-Based Question Answer Models Across 8 Diverse Datasets.
CoRR
Muhammad Muneeb, David B. Ascher, Ahsan Baidar Bakht
2025 — conf
Interpreting Machine Learning Pipelines Produced by Evolutionary AutoML for Biochemical Property Prediction.
GECCO Companion
Alex G. C. de Sá, Gisele L. Pappa, Alex Alves Freitas, David B. Ascher
2024 J jnl
Characterization on the oncogenic effect of the missense mutations of p53 via machine learning.
Briefings Bioinform.
Qisheng Pan, Stephanie Portelli, Thanh-Binh Nguyen, David B. Ascher
2024 — conf
Towards Evolutionary-based Automated Machine Learning for Small Molecule Pharmacokinetic Prediction.
GECCO Companion
Alex G. C. de Sá, David B. Ascher
2024 J jnl
Towards Evolutionary-based Automated Machine Learning for Small Molecule Pharmacokinetic Prediction.
CoRR
Alex G. C. de Sá, David B. Ascher
2024 J jnl
piscesCSM: prediction of anticancer synergistic drug combinations.
J. Cheminformatics
Raghad Al-Jarf, Carlos H. M. Rodrigues, Yoochan Myung, Douglas E. V. Pires, David B. Ascher
2023 J jnl
AI driven B-cell Immunotherapy Design.
CoRR
Bruna Moreira da Silva, David B. Ascher, Nicholas Geard, Douglas E. V. Pires
2023 J jnl
DDMut: predicting effects of mutations on protein stability using deep learning.
Nucleic Acids Res.
Yunzhuo Zhou, Qisheng Pan, Douglas E. V. Pires, Carlos H. M. Rodrigues, David B. Ascher
2023 J jnl
DockNet: high-throughput protein-protein interface contact prediction.
Bioinform.
Nathan P. Williams, Carlos H. M. Rodrigues, Jia Truong, David B. Ascher, Jessica K. Holien
2023 J jnl
Explainable Machine Learning for ICU Readmission Prediction.
CoRR
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
2023 J jnl
LEGO-CSM: a tool for functional characterization of proteins.
Bioinform.
Thanh Binh Nguyen, Alex G. C. de Sá, Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher
2023 J jnl
Understanding the complementarity and plasticity of antibody-antigen interfaces.
Bioinform.
Yoochan Myung, Douglas E. V. Pires, David B. Ascher
2023 J jnl
embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules.
J. Chem. Inf. Model.
Raghad Al-Jarf, Simon Tang, Douglas E. V. Pires, David B. Ascher
2023 J jnl
epitope1D: accurate taxonomy-aware B-cell linear epitope prediction.
Briefings Bioinform.
Bruna Moreira da Silva, David B. Ascher, Douglas E. V. Pires
2022 J jnl
Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93.
Frontiers Bioinform.
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
2022 J jnl
CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function.
Bioinform.
Yoochan Myung, Douglas E. V. Pires, David B. Ascher
2022 J jnl
CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning.
Nucleic Acids Res.
Carlos H. M. Rodrigues, David B. Ascher
2022 J jnl
CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function.
Briefings Bioinform.
Thanh-Binh Nguyen, Douglas E. V. Pires, David B. Ascher
2022 J jnl
Evaluating hierarchical machine learning approaches to classify biological databases.
Briefings Bioinform.
Pâmela M. Rezende, Joicymara S. Xavier, David B. Ascher, Gabriel R. Fernandes, Douglas E. V. Pires
2022 J jnl
GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms.
Briefings Bioinform.
Vinícius de Almeida Paiva, Murillo Ventura Mendonça, Sabrina de Azevedo Silveira, David B. Ascher, Douglas E. V. Pires, Sandro C. Izidoro
2022 J jnl
Known allosteric proteins have central roles in genetic disease.
PLoS Comput. Biol.
György Abrusán, David B. Ascher, Michael Inouye
2022 J jnl
Structural landscapes of PPI interfaces.
Briefings Bioinform.
Carlos H. M. Rodrigues, Douglas E. V. Pires, Tom L. Blundell, David B. Ascher
2022 J jnl
Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures.
Briefings Bioinform.
Qisheng Pan, Thanh-Binh Nguyen, David B. Ascher, Douglas E. V. Pires
2022 J jnl
cropCSM: designing safe and potent herbicides with graph-based signatures.
Briefings Bioinform.
Douglas E. V. Pires, Keith A. Stubbs, Joshua S. Mylne, David B. Ascher
2022 J jnl
epitope3D: a machine learning method for conformational B-cell epitope prediction.
Briefings Bioinform.
Bruna Moreira da Silva, Yoochan Myung, David B. Ascher, Douglas E. V. Pires
2022 J jnl
toxCSM: comprehensive prediction of small molecule toxicity profiles.
Briefings Bioinform.
Alex G. C. de Sá, Yangyang Long, Stephanie Portelli, Douglas E. V. Pires, David B. Ascher
2021 J jnl
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations.
Briefings Bioinform.
Shahid Iqbal, Fuyi Li, Tatsuya Akutsu, David B. Ascher, Geoffrey I. Webb, Jiangning Song
2021 J jnl
Deep learning in diabetic foot ulcers detection: A comprehensive evaluation.
Comput. Biol. Medicine
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
2021 — ch.
Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis.
Artificial Neural Networks, 3rd Edition
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
2021 J jnl
MTR3D: identifying regions within protein tertiary structures under purifying selection.
Nucleic Acids Res.
Michael Silk, Douglas E. V. Pires, Carlos H. M. Rodrigues, Elston N. D'souza, Moshe Olshansky, Natalie Thorne, David B. Ascher
2021 J jnl
ThermoMutDB: a thermodynamic database for missense mutations.
Nucleic Acids Res.
Joicymara S. Xavier, Thanh-Binh Nguyen, Malancha Karmarkar, Stephanie Portelli, Pâmela M. Rezende, João P. L. Velloso, David B. Ascher, Douglas E. V. Pires
2021 J jnl
mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions.
Nucleic Acids Res.
Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher
2021 J jnl
pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors.
J. Chem. Inf. Model.
Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher
2021 J jnl
pdCSM-cancer: Using Graph-Based Signatures to Identify Small Molecules with Anticancer Properties.
J. Chem. Inf. Model.
Raghad Al-Jarf, Alex G. C. de Sá, Douglas E. V. Pires, David B. Ascher
2020 J jnl
Deep Learning in Diabetic Foot Ulcers Detection: A Comprehensive Evaluation.
CoRR
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
2020 J jnl
EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening.
Bioinform.
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
2020 J jnl
ProCarbDB: a database of carbohydrate-binding proteins.
Nucleic Acids Res.
Liviu Copoiu, Pedro H. M. Torres, David B. Ascher, Tom L. Blundell, Sony Malhotra
2020 J jnl
mCSM-AB2: guiding rational antibody design using graph-based signatures.
Bioinform.
Yoochan Myung, Carlos H. M. Rodrigues, David B. Ascher, Douglas E. V. Pires
2020 J jnl
mCSM-membrane: predicting the effects of mutations on transmembrane proteins.
Nucleic Acids Res.
Douglas E. V. Pires, Carlos H. M. Rodrigues, David B. Ascher
2020 J jnl
mmCSM-AB: guiding rational antibody engineering through multiple point mutations.
Nucleic Acids Res.
Yoochan Myung, Douglas E. V. Pires, David B. Ascher
2020 J jnl
mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria.
J. Chem. Inf. Model.
Douglas E. V. Pires, David B. Ascher
2019 J jnl
MTR-Viewer: identifying regions within genes under purifying selection.
Nucleic Acids Res.
Michael Silk, Slavé Petrovski, David B. Ascher
2019 J jnl
mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.
Nucleic Acids Res.
Carlos H. M. Rodrigues, Yoochan Myung, Douglas E. V. Pires, David B. Ascher
2018 J jnl
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability.
Nucleic Acids Res.
Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher
2018 J jnl
Kinact: a computational approach for predicting activating missense mutations in protein kinases.
Nucleic Acids Res.
Carlos H. M. Rodrigues, David B. Ascher, Douglas E. V. Pires
2017 J jnl
SDM: a server for predicting effects of mutations on protein stability.
Nucleic Acids Res.
Arun Prasad Pandurangan, Bernardo Ochoa-Montaño, David B. Ascher, Tom L. Blundell
2017 J jnl
mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions.
Nucleic Acids Res.
Douglas E. V. Pires, David B. Ascher
2016 J jnl
CSM-lig: a web server for assessing and comparing protein-small molecule affinities.
Nucleic Acids Res.
Douglas E. V. Pires, David B. Ascher
2016 J jnl
mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures.
Nucleic Acids Res.
Douglas E. V. Pires, David B. Ascher
2015 J jnl
Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes.
Nucleic Acids Res.
Douglas E. V. Pires, Tom L. Blundell, David B. Ascher
2014 J jnl
DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach.
Nucleic Acids Res.
Douglas E. V. Pires, David B. Ascher, Tom L. Blundell
2014 J jnl
mCSM: predicting the effects of mutations in proteins using graph-based signatures.
Bioinform.
Douglas E. V. Pires, David B. Ascher, Tom L. Blundell