Douglas E. V. Pires

51 papers Journal 48Unranked 2

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Uncovering digital overdiagnosis - Quantification and mitigation using clinical trajectories: Heparin-induced thrombocytopenia use case. J. Biomed. Informatics Prabodi Senevirathna, Douglas E. V. Pires, Daniel Capurro
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`	Adapting Pretrained Language Models for Solving Tabular Prediction Problems in the Electronic Health Record. CoRR Christopher McMaster, David F. L. Liew, 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`	Data-driven overdiagnosis definitions: A scoping review. J. Biomed. Informatics Prabodi Senevirathna, Douglas E. V. Pires, Daniel Capurro
2023	J	`jnl`	Developing a deep learning natural language processing algorithm for automated reporting of adverse drug reactions. J. Biomed. Informatics Christopher McMaster, Julia Chan, David F. L. Liew, Elizabeth Su, Albert G. Frauman, Wendy W. Chapman, Douglas E. V. Pires
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`	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-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`	GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs. Nucleic Acids Res. Charles Abreu Santana, Sandro C. Izidoro, Raquel Cardoso de Melo Minardi, Jonathan D. Tyzack, António J. M. Ribeiro, Douglas E. V. Pires, Janet M. Thornton, Sabrina de Azevedo Silveira
2022	J	`jnl`	Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. BMC Bioinform. Aparna Elangovan, Yuan Li, Douglas E. V. Pires, Melissa J. Davis, Karin Verspoor
2022	J	`jnl`	Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. CoRR Aparna Elangovan, Yuan Li, Douglas E. V. Pires, Melissa J. Davis, Karin Verspoor
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	—	`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`	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`	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`	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`	GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms. Nucleic Acids Res. João P. A. Moraes, Gisele L. Pappa, Douglas E. V. Pires, Sandro C. Izidoro
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`	PDBest: a user-friendly platform for manipulating and enhancing protein structures. Bioinform. Wellisson R. S. Gonçalves, Valdete M. Gonçalves-Almeida, Aleksander L. Arruda, Wagner Meira Jr., Carlos Henrique da Silveira, Douglas E. V. Pires, Raquel Cardoso de Melo Minardi
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
2013	J	`jnl`	aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction. Bioinform. Douglas E. V. Pires, Raquel Cardoso de Melo Minardi, Carlos Henrique da Silveira, Frederico F. Campos, Wagner Meira Jr.
2012	J	`jnl`	FPCluster: An Efficient Out-of-core Clustering Strategy without a Similarity Metric. J. Inf. Data Manag. Douglas E. V. Pires, Luam C. Totti, Rubens E. A. Moreira, Elverton C. Fazzion, Osvaldo L. H. M. Fonseca, Wagner Meira Jr., Raquel Cardoso de Melo Minardi, Dorgival Olavo Guedes Neto
2012	J	`jnl`	HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids. Bioinform. Valdete M. Gonçalves-Almeida, Douglas E. V. Pires, Raquel Cardoso de Melo Minardi, Carlos Henrique da Silveira, Wagner Meira Jr., Marcelo M. Santoro
2011	—	`conf`	FPCluster: Uma estratégia eficiente de agrupamento out-of-core sem medida de similaridade. SBBD (Short Papers) Douglas E. V. Pires, Luam C. Totti, Rubens E. A. Moreira, Elverton C. Fazzion, Osvaldo L. H. M. Fonseca, Wagner Meira Jr., Raquel Cardoso de Melo Minardi, Dorgival O. Guedes
2008	—	`conf`	A Campaign-based Characterization of Spamming Strategies. CEAS Pedro H. Calais, Douglas E. V. Pires, Dorgival Olavo Guedes Neto, Wagner Meira Jr., Cristine Hoepers, Klaus Steding-Jessen