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2020 – today
- 2024
[j42]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): 81 (2024)- [c5]Prabodi Senevirathna
, Douglas Pires, Daniel Capurro:
Clinical Translation of a Heparin-Induced Thrombocytopenia predictor for Intensive Care Patients. ACSW 2024: 124-129 - [i7]Henry Kenlay, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, Charlotte M. Deane:
Large scale paired antibody language models. CoRR abs/2403.17889 (2024) - 2023
- [j41]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) - [j40]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: 104265 (2023) - [j39]Prabodi Senevirathna, Douglas E. V. Pires, Daniel Capurro:
Data-driven overdiagnosis definitions: A scoping review. J. Biomed. Informatics 147: 104506 (2023) - [j38]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): 432-441 (2023) - [j37]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): 122-128 (2023) - [c4]Sathana Dushyanthen, Dawn Choo, Meg Perrier, Kathleen Gray, Daniel Capurro, Douglas Pires, Brian E. Chapman, Graeme K. Hart, Kit Huckvale, Wendy W. Chapman, Kayley M. Lyons:
Designing an Interprofessional Online Course to Foster Learning Health Systems. MedInfo 2023: 1241-1245 - [i6]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 abs/2303.14920 (2023) - [i5]Bruna Moreira da Silva, David B. Ascher, Nicholas Geard, Douglas E. V. Pires:
AI driven B-cell Immunotherapy Design. CoRR abs/2309.01122 (2023) - [i4]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 abs/2309.13781 (2023) - [i3]Marius Urbonas, Temitope Ajileye, Paul Gainer, Douglas Pires:
Automating reward function configuration for drug design. CoRR abs/2312.09865 (2023) - 2022
- [j36]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) - [j35]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) - [j34]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) - [j33]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) - [j32]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) - [j31]Carlos H. M. Rodrigues, Douglas E. V. Pires, Tom L. Blundell, David B. Ascher:
Structural landscapes of PPI interfaces. Briefings Bioinform. 23(4) (2022) - [j30]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) - [j29]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) - [j28]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): 1141-1143 (2022) - [j27]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): 4 (2022) - [j26]Saba Iftkhar, Alex G. C. de Sá, João P. L. Velloso, Raghad Al-Jarf, Douglas E. V. Pires, David B. Ascher:
cardioToxCSM: A Web Server for Predicting Cardiotoxicity of Small Molecules. J. Chem. Inf. Model. 62(20): 4827-4836 (2022) - [j25]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): 392-397 (2022) - [i2]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 abs/2201.02229 (2022) - 2021
- [j24]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): 3314-3322 (2021) - [j23]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): 5438-5445 (2021) - [j22]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): D475-D479 (2021) - [j21]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): 417-424 (2021) - [j20]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): 438-445 (2021) - [c3]Anna Fedyukova, Douglas Pires, Daniel Capurro:
A comparative analysis of sepsis digital phenotyping methods. ACSW 2021: 19:1-19:4 - [p1]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:
Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis. Artificial Neural Networks, 3rd Edition 2021: 1-32 - [i1]Anna Fedyukova, Douglas Pires, Daniel Capurro:
Quantifying machine learning-induced overdiagnosis in sepsis. CoRR abs/2107.10399 (2021) - 2020
- [j19]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): 1453-1459 (2020) - [j18]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): 4200-4202 (2020) - [j17]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): 3450-3456 (2020) - [j16]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): W125-W131 (2020) - [j15]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): W147-W153 (2020)
2010 – 2019
- 2019
- [j14]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): W338-W344 (2019) - 2018
- [j13]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): W127-W132 (2018) - [j12]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): W350-W355 (2018) - 2017
- [j11]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): W241-W246 (2017) - [j10]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): W315-W319 (2017) - 2016
- [j9]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): W469-W473 (2016) - [j8]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): W557-W561 (2016) - 2015
- [j7]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): 2894-2896 (2015) - [j6]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): 387-391 (2015) - 2014
- [j5]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): 335-342 (2014) - [j4]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): 314-319 (2014) - 2013
- [j3]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): 855-861 (2013) - 2012
- [j2]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): 342-349 (2012) - [j1]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): 132-141 (2012) - 2011
- [c2]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: 97-104
2000 – 2009
- 2008
- [c1]Pedro H. 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
Coauthor Index
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