Raquel Cardoso de Melo Minardi

51 papers A 1C 3Misc 1Journal 23Unranked 21

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices. Frontiers Bioinform. Rafael P. Lemos, Diego C. B. Mariano, Sabrina de Azevedo Silveira, Raquel Cardoso de Melo Minardi
2024	—	`conf`	A strategy for refining the calculation of contacts in protein-RNA complexes. BSB Luana Luiza Bastos, Rafael P. Lemos, Diego C. B. Mariano, Raquel Cardoso de Melo Minardi
2024	—	`conf`	COCαDA - Large-Scale Protein Interatomic Contact Cutoff Optimization by Cα Distance Matrices. BSB Rafael P. Lemos, Diego C. B. Mariano, Sabrina de Azevedo Silveira, Raquel Cardoso de Melo Minardi
2024	—	`conf`	Predicting Mutation-Driven Changes in the SARS-CoV-2 Spike Protein Using Structural Signatures and Neural Networks. BSB Eduardo U. M. Moreira, Leandro Morais, Sheila Cruz Araujo, Rafael P. Lemos, Ana Luísa A. Bastos, Alessandra Lima da Silva, Diego C. B. Mariano, Raquel Cardoso de Melo Minardi
2024	—	`conf`	Teaching bioinformatics programming in high school: a case report. BSB Helena Lott Costa, Giovana C. F. Maia, Lucas G. S. Chaves, Diego C. B. Mariano, Raquel Cardoso de Melo Minardi
2024	—	`conf`	Using graph-based structural signatures and machine learning algorithms for molecular docking assessment of histone deacetylases and small ligands. BSB Alessandra Gomes Cioletti, Rafael P. Lemos, Lucas Moraes dos Santos, Diego C. B. Mariano, Raquel Cardoso de Melo Minardi
2024	C	`conf`	ViPeC: Vision transformer-based approach for Peptide-protein interface Classification. CIBCB Lucas Moraes dos Santos, Diego C. B. Mariano, Raquel Cardoso de Melo Minardi
2023	—	`ed.`	Advances in Bioinformatics and Computational Biology - 16th Brazilian Symposium on Bioinformatics, BSB 2023, Curitiba, Brazil, June 13-16, 2023, Proceedings BSB Marcelo da Silva Reis, Raquel Cardoso de Melo Minardi
2023	J	`jnl`	Editorial: Bioinformatics in the age of data science: algorithms, methods, and tools applied from Omics to structural data. Frontiers Bioinform. Diego C. B. Mariano, Néli José da Fonseca Jr., Lucianna Helene Santos, Raquel Cardoso de Melo Minardi
2023	J	`jnl`	Know-how of holding a Bioinformatics competition: Structure, model, overview, and perspectives. PLoS Comput. Biol. Elvira C. A. Horácio, Lucas M. de Carvalho, Gustavo G. Pereira, Mayla C. Abrahim, Mônica P. Coelho, Deivid Almeida de Jesus, Glen J. Y. García, Raquel Cardoso de Melo Minardi, Sheila T. Nagamatsu
2023	—	`conf`	Peptide-Protein Interface Classification Using Convolutional Neural Networks. BSB Lucas Moraes dos Santos, Diego C. B. Mariano, Luana Luiza Bastos, Alessandra Gomes Cioletti, Raquel Cardoso de Melo Minardi
2023	J	`jnl`	Propedia v2.3: A novel representation approach for the peptide-protein interaction database using graph-based structural signatures. Frontiers Bioinform. Pedro Martins, Diego C. B. Mariano, Frederico Chaves Carvalho, Luana Luiza Bastos, Lucas Moraes, Vivian Morais Paixão, Raquel Cardoso de Melo Minardi
2023	—	`conf`	Using Natural Language Processing for Context Identification in COVID-19 Literature. BSB Frederico Chaves Carvalho, Diego C. B. Mariano, Marcos Bomfim, Giovana Fiorini, Luana L. Bastos, Ana Paula de Abreu, Vivian Paixão, Lucas Moraes dos Santos, Juliana Silva, Angie Puelles, Alessandra Lima da Silva, Raquel Cardoso de Melo Minardi
2022	—	`ed.`	Advances in Bioinformatics and Computational Biology - 15th Brazilian Symposium on Bioinformatics, BSB 2022, Buzios, Brazil, September 21-23, 2022, Proceedings BSB Nicole M. Scherer, Raquel Cardoso de Melo Minardi
2022	—	`conf`	Computational Methodology for Discovery of Potential Inhibitory Peptides. BSB Vivian Morais Paixão, Raquel Cardoso de Melo Minardi
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	—	`conf`	Identifying Large Scale Conformational Changes in Proteins Through Distance Maps and Convolutional Networks. BSB Lucas Moraes dos Santos, Raquel Cardoso de Melo Minardi
2022	J	`jnl`	Prioritizing Virtual Screening with Interpretable Interaction Fingerprints. J. Chem. Inf. Model. Alexandre V. Fassio, Laura Shub, Luca Ponzoni, Jessica McKinley, Matthew J. O'Meara, Rafaela Salgado Ferreira, Michael J. Keiser, Raquel Cardoso de Melo Minardi
2022	J	`jnl`	Protein structural bioinformatics: An overview. Comput. Biol. Medicine Vinícius de Almeida Paiva, Isabela de Souza Gomes, Cleiton Rodrigues Monteiro, Murillo Ventura Mendonça, Pedro Magalhães Martins, Charles Abreu Santana, Valdete M. Gonçalves-Almeida, Sandro Carvalho Izidoro, Raquel Cardoso de Melo Minardi, Sabrina de Azevedo Silveira
2021	J	`jnl`	From In-Person to the Online World: Insights Into Organizing Events in Bioinformatics. Frontiers Bioinform. Alessandra Lima da Silva, Ana Paula de Abreu, Diego C. B. Mariano, Felipe Caixeta, Fenícia Brito Santos, Fernanda Stussi D. Lage, Gabriel Quintanilha-Peixoto, Heron O. Hilário, Joicymara S. Xavier, Lucio R. Queiroz, Nayara Evelin de Toledo, Raphael Tavares, Rodrigo Bentes Kato, Roselane Gonçalves dos Santos, Stellamaris Soares, Wanessa M. Goes, Wylerson Guimarães Nogueira, Thiago M. Batista, José Miguel Ortega, Vasco Ariston Azevedo De Carvalho, Glória Regina Franco, Raquel Cardoso de Melo Minardi, Aristóteles Góes-Neto
2021	J	`jnl`	Propedia: a database for protein-peptide identification based on a hybrid clustering algorithm. BMC Bioinform. Pedro M. Martins, Lucianna Helene Santos, Diego C. B. Mariano, Felippe C. Queiroz, Luana L. Bastos, Isabela de Souza Gomes, Pedro H. C. Fischer, Rafael E. O. Rocha, Sabrina de Azevedo Silveira, Leonardo H. F. de Lima, Mariana T. Q. de Magalhães, Maria G. A. Oliveira, Raquel Cardoso de Melo Minardi
2021	J	`jnl`	VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes. Frontiers Bioinform. Vitor Pimentel, Diego C. B. Mariano, Letícia Xavier Silva Cantão, Luana Luiza Bastos, Pedro H. C. Fischer, Leonardo Henrique Franca de Lima, Alexandre Victor Fassio, Raquel Cardoso de Melo Minardi
2020	—	`conf`	A Brief History of Bioinformatics Told by Data Visualization. BSB Diego C. B. Mariano, Mívian M. Ferreira, Bruno Luan de Sousa, Lucianna Helene Santos, Raquel Cardoso de Melo Minardi
2020	J	`jnl`	GRaSP: a graph-based residue neighborhood strategy to predict binding sites. Bioinform. Charles Abreu Santana, Sabrina de Azevedo Silveira, João P. A. Moraes, Sandro C. Izidoro, Raquel Cardoso de Melo Minardi, António J. M. Ribeiro, Jonathan D. Tyzack, Neera Borkakoti, Janet M. Thornton
2020	J	`jnl`	Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures. BMC Bioinform. José Renato M. S. Barroso, Diego C. B. Mariano, Sandro R. Dias, Rafael E. O. Rocha, Lucianna Helene Santos, Ronaldo Alves Pinto Nagem, Raquel Cardoso de Melo Minardi
2020	J	`jnl`	nAPOLI: A Graph-Based Strategy to Detect and Visualize Conserved Protein-Ligand Interactions in Large-Scale. IEEE ACM Trans. Comput. Biol. Bioinform. Alexandre V. Fassio, Lucianna Helene Santos, Sabrina de Azevedo Silveira, Rafaela Salgado Ferreira, Raquel Cardoso de Melo Minardi
2019	—	`conf`	Protein Structural Signatures Revisited: Geometric Linearity of Main Chains are More Relevant to Classification Performance than Packing of Residues. IWBBIO (1) João Arthur F. Gadelha Campelo, Cleiton Rodrigues Monteiro, Carlos Henrique da Silveira, Sabrina de Azevedo Silveira, Raquel Cardoso de Melo Minardi
2019	J	`jnl`	Proteingo: Motivation, user experience, and learning of molecular interactions in biological complexes. Entertain. Comput. Marcos Felipe Martins Silva, Pedro M. Martins, Diego C. B. Mariano, Lucianna Helene Santos, Isabela Pastorini, Naiara Pantuza, Cristiane Neri Nobre, Raquel Cardoso de Melo Minardi
2018	—	`conf`	An Interactive Strategy to Visualize Common Subgraphs in Protein-Ligand Interaction. IWBBIO (1) Alexandre V. Fassio, Charles Abreu Santana, Fabio Ribeiro Cerqueira, Carlos Henrique da Silveira, João P. R. Romanelli, Raquel Cardoso de Melo Minardi, Sabrina de Azevedo Silveira
2018	Misc	`conf`	How to compute protein residue contacts more accurately? SAC Pedro M. Martins, Vinícius D. Mayrink, Sabrina de Azevedo Silveira, Carlos Henrique da Silveira, Leonardo H. F. de Lima, Raquel Cardoso de Melo Minardi
2017	C	`conf`	CALI: A Novel Visual Model for Frequent Pattern Mining in Protein-Ligand Graphs. BIBE Susana Medina G., Alexandre Victor Fassio, Sabrina de Azevedo Silveira, Carlos Henrique da Silveira, Raquel Cardoso de Melo Minardi
2017	—	`conf`	Experimental Evaluation of Crowdsourcing on the Characterization of Data Visualization Techniques. BRACIS Geraldo Ribeiro Franciscani, Rodrygo L. T. Santos, Michel Boaventura, Pedro Dalla Bernardina, Wagner Meira Jr., Raquel Cardoso de Melo Minardi
2017	—	`conf`	Portinari: A Data Exploration Tool to Personalize Cervical Cancer Screening. ICSE-SEIS Sagar Sen, Manoel Horta Ribeiro, Raquel Cardoso de Melo Minardi, Wagner Meira Jr., Mari Nygård
2017	J	`jnl`	Portinari: A Data Exploration Tool to Personalize Cervical Cancer Screening. CoRR Sagar Sen, Manoel Horta Ribeiro, Raquel Cardoso de Melo Minardi, Wagner Meira Jr., Mari Nygård
2017	J	`jnl`	Vermont: a multi-perspective visual interactive platform for mutational analysis. BMC Bioinform. Alexandre V. Fassio, Pedro M. Martins, Samuel da Silva Guimarães, Sócrates S. A. Junior, Vagner S. Ribeiro, Raquel Cardoso de Melo Minardi, Sabrina de Azevedo Silveira
2016	—	`conf`	Emotional Fingerprint from Authors in Classical Literature. WebMedia Matheus Lima Diniz Araújo, Iuro B. P. Nascimento, Gustavo Caetano Rafael, Raquel Cardoso de Melo Minardi, Fabrício Benevenuto
2016	C	`conf`	GReMLIN: A Graph Mining Strategy to Infer Protein-Ligand Interaction Patterns. BIBE Charles Abreu Santana, Fabio Ribeiro Cerqueira, Carlos Henrique da Silveira, Alexandre V. Fassio, Raquel Cardoso de Melo Minardi, Sabrina de Azevedo Silveira
2016	J	`jnl`	Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering. PLoS Comput. Biol. Elisa Boari de Lima, Wagner Meira Jr., Raquel Cardoso de Melo Minardi
2015	J	`jnl`	GASS: identifying enzyme active sites with genetic algorithms. Bioinform. Sandro C. Izidoro, Raquel Cardoso de Melo Minardi, Gisele L. Pappa
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
2014	—	`conf`	Uma investigação sobre as técnicas de visualização de informação quantitativas e qualitativas. IHC Diego Barros, Raquel Oliveira Prates, Raquel Cardoso de Melo Minardi
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.
2013	—	`conf`	uTrack: track yourself! monitoring information on online social media. WWW (Companion Volume) Tiago Rodrigues, Prateek Dewan, Ponnurangam Kumaraguru, Raquel Cardoso de Melo Minardi, Virgílio A. F. Almeida
2012	—	`conf`	ADVISe: Visualizing the dynamics of enzyme annotations in UniProt/Swiss-Prot. BioVis Sabrina de Azevedo Silveira, Artur O. Rodrigues, Raquel Cardoso de Melo Minardi, Carlos Henrique da Silveira, Wagner Meira Jr.
2012	—	`conf`	Combining traditional and high-density visualizations in a dashboard to network health monitoring. IEEE VAST Yussif Barcelos, Flavia Aburjaile, Laura R. Leite, Solange T. Oliveira, Raquel Cardoso de Melo Minardi
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	A	`conf`	Data Integration via Constrained Clustering: An Application to Enzyme Clustering. SDM Elisa Boari de Lima, Raquel Cardoso de Melo Minardi, Wagner Meira Jr., Mohammed Javeed Zaki
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
2011	—	`conf`	GreenWiki: a tool to support users' assessment of the quality of Wikipedia articles. JCDL Daniel Hasan Dalip, Raquel Lara dos Santos, Diogo Rennó Rocha de Oliveira, Valéria Freitas Amaral, Marcos André Gonçalves, Raquel Oliveira Prates, Raquel Cardoso de Melo Minardi, Jussara Marques de Almeida
2010	J	`jnl`	Identification of subfamily-specific sites based on active sites modeling and clustering. Bioinform. Raquel Cardoso de Melo Minardi, Karine Bastard, François Artiguenave