Douglas E. V. Pires

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 39

Top Topics

Protein Structure

Neighborhood Graph

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

J. Chem. Inf. Model.

Publications

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)
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)
Christopher McMaster, David F. L. Liew, Douglas E. V. Pires
Adapting Pretrained Language Models for Solving Tabular Prediction Problems in the Electronic Health Record. CoRR (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)
Christopher McMaster, Julia Chan, David F. L. Liew, Elizabeth Su, Albert G. Frauman, Wendy W. Chapman, Douglas E. V. Pires
Developing a deep learning natural language processing algorithm for automated reporting of adverse drug reactions. J. Biomed. Informatics 137 (2023)
Bruna Moreira da Silva, David B. Ascher, Nicholas Geard, Douglas E. V. Pires
AI driven B-cell Immunotherapy Design. CoRR (2023)
Prabodi Senevirathna, Douglas E. V. Pires, Daniel Capurro
Data-driven overdiagnosis definitions: A scoping review. J. Biomed. Informatics 147 (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)
Aparna Elangovan, Yuan Li, Douglas E. V. Pires, Melissa J. Davis, Karin Verspoor
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. BMC Bioinform. 23 (1) (2022)
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
GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs. Nucleic Acids Res. 50 (W1) (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)
Aparna Elangovan, Yuan Li, Douglas E. V. Pires, Melissa J. Davis, Karin Verspoor
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. CoRR (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)
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)
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)
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)
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)
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)
João P. A. Moraes, Gisele L. Pappa, Douglas E. V. Pires, Sandro C. Izidoro
GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms. 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)
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
PDBest: a user-friendly platform for manipulating and enhancing protein structures. Bioinform. 31 (17) (2015)
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)
Douglas E. V. Pires, Raquel Cardoso de Melo Minardi, Carlos Henrique da Silveira, Frederico F. Campos, Wagner Meira Jr.
aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction. Bioinform. 29 (7) (2013)
Valdete M. Gonçalves-Almeida, Douglas E. V. Pires, Raquel Cardoso de Melo Minardi, Carlos Henrique da Silveira, Wagner Meira Jr., Marcelo M. Santoro
HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids. Bioinform. 28 (3) (2012)
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
FPCluster: An Efficient Out-of-core Clustering Strategy without a Similarity Metric. J. Inf. Data Manag. 3 (2) (2012)
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
FPCluster: Uma estratégia eficiente de agrupamento out-of-core sem medida de similaridade. SBBD (Short Papers) (2011)
Pedro Calais, Douglas E. V. Pires, Dorgival Olavo Guedes Neto, Wagner Meira Jr., Cristine Hoepers, Klaus Steding-Jessen
A Campaign-based Characterization of Spamming Strategies. CEAS (2008)