mCSM: predicting the effects of mutations in proteins using graph-based signatures. - Douglas E. V. Pires; David B. Ascher; Tom L. Blundell (Bioinform., 2014)

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. - Douglas E. V. Pires; David B. Ascher; Tom L. Blundell (Nucleic Acids Res., 2014)

Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. - Douglas E. V. Pires; Tom L. Blundell; David B. Ascher (Nucleic Acids Res., 2015)

mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures. - Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2016)

CSM-lig: a web server for assessing and comparing protein-small molecule affinities. - Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2016)

SDM: a server for predicting effects of mutations on protein stability. - Arun Prasad Pandurangan; Bernardo Ochoa-Montaño; David B. Ascher; Tom L. Blundell (Nucleic Acids Res., 2017)

mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions. - Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2017)

Kinact: a computational approach for predicting activating missense mutations in protein kinases. - Carlos H. M. Rodrigues; David B. Ascher; Douglas E. V. Pires (Nucleic Acids Res., 2018)

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. - Carlos H. M. Rodrigues; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2018)

mCSM-PPI2: predicting the effects of mutations on protein-protein interactions. - Carlos H. M. Rodrigues; Yoochan Myung; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2019)

MTR-Viewer: identifying regions within genes under purifying selection. - Michael Silk; Slavé Petrovski; David B. Ascher (Nucleic Acids Res., 2019)

mCSM-AB2: guiding rational antibody design using graph-based signatures. - Yoochan Myung; Carlos H. M. Rodrigues; David B. Ascher; Douglas E. V. Pires (Bioinform., 2020)

EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening. - 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 (Bioinform., 2020)

mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria. - Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2020)

ProCarbDB: a database of carbohydrate-binding proteins. - Liviu Copoiu; Pedro H. M. Torres; David B. Ascher; Tom L. Blundell; Sony Malhotra (Nucleic Acids Res., 2020)

mmCSM-AB: guiding rational antibody engineering through multiple point mutations. - Yoochan Myung; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2020)

mCSM-membrane: predicting the effects of mutations on transmembrane proteins. - Douglas E. V. Pires; Carlos H. M. Rodrigues; David B. Ascher (Nucleic Acids Res., 2020)

Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis. - 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; et al. (Artificial Neural Networks, 3rd Edition, 2021)

Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. - Shahid Iqbal; Fuyi Li; Tatsuya Akutsu; David B. Ascher; Geoffrey I. Webb; Jiangning Song (Briefings Bioinform., 2021)

Deep learning in diabetic foot ulcers detection: A comprehensive evaluation. - 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; et al. (Comput. Biol. Medicine, 2021)

pdCSM-cancer: Using Graph-Based Signatures to Identify Small Molecules with Anticancer Properties. - Raghad Al-Jarf; Alex G. C. de Sá; Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2021)

pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors. - Carlos H. M. Rodrigues; Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2021)

mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions. - Carlos H. M. Rodrigues; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2021)

MTR3D: identifying regions within protein tertiary structures under purifying selection. - Michael Silk; Douglas E. V. Pires; Carlos H. M. Rodrigues; Elston N. D'souza; Moshe Olshansky; Natalie Thorne; David B. Ascher (Nucleic Acids Res., 2021)

ThermoMutDB: a thermodynamic database for missense mutations. - Joicymara S. Xavier; Thanh-Binh Nguyen 007; Malancha Karmarkar; Stephanie Portelli; Pâmela M. Rezende; João P. L. Velloso; David B. Ascher; Douglas E. V. Pires (Nucleic Acids Res., 2021)

CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function. - Thanh-Binh Nguyen 007; Douglas E. V. Pires; David B. Ascher (Briefings Bioinform., 2022)

GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms. - Vinícius de Almeida Paiva; Murillo Ventura Mendonça; Sabrina de Azevedo Silveira; David B. Ascher; Douglas E. V. Pires; Sandro C. Izidoro (Briefings Bioinform., 2022)

Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. - Qisheng Pan; Thanh-Binh Nguyen 007; David B. Ascher; Douglas E. V. Pires (Briefings Bioinform., 2022)

cropCSM: designing safe and potent herbicides with graph-based signatures. - Douglas E. V. Pires; Keith A. Stubbs; Joshua S. Mylne; David B. Ascher (Briefings Bioinform., 2022)

Evaluating hierarchical machine learning approaches to classify biological databases. - Pâmela M. Rezende; Joicymara S. Xavier; David B. Ascher; Gabriel R. Fernandes; Douglas E. V. Pires (Briefings Bioinform., 2022)

Structural landscapes of PPI interfaces. - Carlos H. M. Rodrigues; Douglas E. V. Pires; Tom L. Blundell; David B. Ascher (Briefings Bioinform., 2022)

toxCSM: comprehensive prediction of small molecule toxicity profiles. - Alex G. C. de Sá; Yangyang Long; Stephanie Portelli; Douglas E. V. Pires; David B. Ascher (Briefings Bioinform., 2022)

epitope3D: a machine learning method for conformational B-cell epitope prediction. - Bruna Moreira da Silva; Yoochan Myung; David B. Ascher; Douglas E. V. Pires (Briefings Bioinform., 2022)

CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function. - Yoochan Myung; Douglas E. V. Pires; David B. Ascher (Bioinform., 2022)

Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93. - 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; et al. (Frontiers Bioinform., 2022)

cardioToxCSM: A Web Server for Predicting Cardiotoxicity of Small Molecules. - Saba Iftkhar; Alex G. C. de Sá; João P. L. Velloso; Raghad Al-Jarf; Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2022)

CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. - Carlos H. M. Rodrigues; David B. Ascher (Nucleic Acids Res., 2022)

Known allosteric proteins have central roles in genetic disease. - György Abrusán; David B. Ascher; Michael Inouye (PLoS Comput. Biol., 2022)

AI driven B-cell Immunotherapy Design. - Bruna Moreira da Silva; David B. Ascher; Nicholas Geard; Douglas E. V. Pires (CoRR, 2023)

Explainable Machine Learning for ICU Readmission Prediction. - 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 (CoRR, 2023)

DockNet: high-throughput protein-protein interface contact prediction. - Nathan P. Williams; Carlos H. M. Rodrigues; Jia Truong; David B. Ascher; Jessica K. Holien (Bioinform., 2023)

embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules. - Raghad Al-Jarf; Simon Tang; Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2023)

epitope1D: accurate taxonomy-aware B-cell linear epitope prediction. - Bruna Moreira da Silva; David B. Ascher; Douglas E. V. Pires (Briefings Bioinform., 2023)

DDMut: predicting effects of mutations on protein stability using deep learning. - Yunzhuo Zhou; Qisheng Pan; Douglas E. V. Pires; Carlos H. M. Rodrigues; David B. Ascher (Nucleic Acids Res., 2023)

Characterization on the oncogenic effect of the missense mutations of p53 via machine learning. - Qisheng Pan; Stephanie Portelli; Thanh-Binh Nguyen 007; David B. Ascher (Briefings Bioinform., 2023)

Towards Evolutionary-based Automated Machine Learning for Small Molecule Pharmacokinetic Prediction. - Alex G. C. de Sá; David B. Ascher (GECCO Companion, 2024)

piscesCSM: prediction of anticancer synergistic drug combinations. - Raghad Al-Jarf; Carlos H. M. Rodrigues; Yoochan Myung; Douglas E. V. Pires; David B. Ascher (J. Cheminformatics, 2024)

Auto-ADMET: An Effective and Interpretable AutoML Method for Chemical ADMET Property Prediction. - Alex G. C. de Sá; David B. Ascher (CoRR, 2025)