Publications

Computational prediction of potential inhibitors for SARS-COV-2 main protease based on machine learning, docking, MM-PBSA calculations, and metadynamics

Gomes, I. D. S., Santana, C. A., Marcolino, L. S., Lima, L. H. F. D., Melo-Minardi, R. C. D., Dias, R. S., Paula, S. O., & Silveira, S. D. A.
Plos one (2022)

DOI: 10.1371/journal.pone.0267471

GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms

Paiva, V. A., Mendonça, M. V., Silveira, S. A., Ascher, D. B., Pires, D. E., & Izidoro, S. C.
Briefings in Bioinformatics (2022)

DOI: 10.1093/bib/bbac178

Protein structural bioinformatics: An overview

Paiva, V. A., Gomes, I. D. S., Monteiro, C. R., Mendonça, M. V., Martins, P. M., Santana, C. A., Gonçalves-Almeida, V., Izidoro, S. C., & de Azevedo Silveira, S.
Computers in Biology and Medicine (2022)

DOI: 10.1016/j.compbiomed.2022.105695

RLPredictiOme, a Machine Learning-Derived Method for High-Throughput Prediction of Plant Receptor-like Proteins, Reveals Novel Classes of Transmembrane Receptors

Silva, J. C. F., Ferreira, M. A., Carvalho, T. F., Silva, F. F., de A. Silveira, S., Brommonschenkel, S. H., & Fontes, E. P.
International Journal of Molecular Sciences (2022)

DOI: 10.3390/ijms232012176

GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs

Santana, C. A., Izidoro, S. C., de Melo-Minardi, R. C., Tyzack, J. D., Ribeiro, A. J., Pires, D. E., Thornton, J. M, & de A. Silveira, S.
Nucleic Acids Research (2022)

DOI: 10.1093/nar/gkac323

Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm

Martins, P. M., Santos, L. H., Mariano, D., Queiroz, F. C., Bastos, L. L., Gomes, I. D. S., Fischer, P. H. C., Rocha, R. E. O., Silveira, S. A., de Lima, L. H. F., de Magalhães, M. T. Q., Oliveira, M. G. A., & de Melo-Minardi, R. C.
BMC bioinformatics (2021)

DOI: 10.1186/s12859-020-03881-z

Protein Abundance Prediction Through Machine Learning Methods

Ferreira, M., Ventorim, R., Almeida, E., Silveira, S., & Silveira, W.
Journal of molecular biology (2021)

DOI: 10.1016/j.jmb.2021.167267

visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level

Ribeiro, V. S., Santana, C. A., Fassio, A. V., Cerqueira, F. R., da Silveira, C. H., Romanelli, J. P., Patarroyo-Vargas, A., Oliveira, M. G. A., Gonçalves-Almeida, V., Izidoro S. C., de Melo-Minardi R. C. & Silveira, S. D. A.
BMC bioinformatics (2020)

DOI: 10.1186/s12859-020-3347-7

ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces

Queiroz, F. C., Vargas, A. M., Oliveira, M. G., Comarela, G. V., & Silveira, S. A.
BMC bioinformatics (2020)

DOI: 10.1186/s12859-020-3474-1

GRaSP: a graph-based residue neighborhood strategy to predict binding sites

Santana, C. A., Silveira, S. D. A., Moraes, J. P., Izidoro, S. C., de Melo-Minardi, R. C., Ribeiro, A. J., Tyzack, J. D., Borkakoti, N., & Thornton, J. M.
Bioinformatics (2020)

DOI: 10.1093/bioinformatics/btaa805

nAPOLI: A Graph-Based Strategy to Detect and Visualize Conserved Protein-Ligand Interactions in Large-Scale

Fassio, A. V., Santos, L. H., Silveira, S. A., Ferreira, R. S., & de Melo-Minardi, R. C.
IEEE/ACM transactions on computational biology and bioinformatics (2019)

DOI: 10.1109/TCBB.2019.2892099

Vermont: a multi-perspective visual interactive platform for mutational analysis

Fassio, A. V., Martins, P. M., Guimarães, S. D. S., Junior, S. S., Ribeiro, V. S., de Melo-Minardi, R. C., & Silveira, S. D. A.
BMC bioinformatics (2017)

DOI: 10.1186/s12859-017-1789-3

ENZYMAP: Exploiting Protein Annotation for Modeling and Predicting EC Number Changes in UniProt/Swiss-Prot

Silveira, S. D. A., de Melo-Minardi, R. C., da Silveira, C. H., Santoro, M. M., & Meira Jr, W.
PloS one (2014)

DOI: 10.1371/journal.pone.0089162

VERMONT: Visualizing mutations and their effects on protein physicochemical and topological property conservation

Silveira, S. A., Fassio, A. V., Gonçalves-Almeida, V. M., de Lima, E. B., Barcelos, Y. T., Aburjaile, F. F., Rodrigues, L. M., Meira Jr, W., & de Melo-Minardi, R. C.
BMC proceedings (2014)

DOI: 10.1186/1753-6561-8-S2-S4

Conference Papers

A Hierarchical and Scalable Strategy for Protein Structural Classification

Mendes, V. F., Monteiro, C. R., Comarela, G. V., & Silveira, S. A.
International Work-Conference on Bioinformatics and Biomedical Engineering (2019)

DOI: 10.1007/978-3-030-17938-0_34

Protein Structural Signatures Revisited: Geometric Linearity of Main Chains are More Relevant to Classification Performance than Packing of Residues

Gadelha Campelo, J. A. F., Rodrigues Monteiro, C., Silveira, C. H. D., Azevedo Silveira, S. D., & Cardoso de Melo-Minardi, R.
International Work-Conference on Bioinformatics and Biomedical Engineering (2019)

DOI: 10.1007/978-3-030-17938-0_35

How to compute protein residue contacts more accurately?

Martins, P. M., Mayrink, V. D., de A. Silveira, S., da Silveira, C. H., de Lima, L. H., & de Melo-Minardi, R. C.
Proceedings of the 33rd Annual ACM Symposium on Applied Computing (2018)

DOI: 10.1145/3167132.3167136

Using supervised learning successful descriptors to perform protein structural classification through unsupervised learning

Monteiro, C., Mendes, V., Comarela, G., & Silveira, S. A.
IEEE International Conference on Bioinformatics and Biomedicine (2018)

DOI: 10.1109/BIBM.2018.8621332

An Interactive Strategy to Visualize Common Subgraphs in Protein-Ligand Interaction

Fassio, A. V., Santana, C. A., Cerqueira, F. R., Silveira, C. H. D., Romanelli, J. P., Melo-Minardi, R. C. D., & Silveira, S. D. A.
International Conference on Bioinformatics and Biomedical Engineering (2018)

DOI: 10.1007/978-3-319-78723-7_33

CALI: A Novel Visual Model for Frequent Pattern Mining in Protein-Ligand Graphs

Medina, S. G., Fassio, A. V., Silveira, S. D. A., da Silveira, C. H., & de Melo-Minardi, R. C.
IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) (2017)

DOI: 10.1109/BIBE.2017.00-29

GReMLIN: A Graph Mining Strategy to Infer Protein-Ligand Interaction Patterns

Santana, C. A., Cerqueira, F. R., Da Silveira, C. H., Fassio, A. V., de Melo-Minardi, R. C., & Silveira, S. D. A.
IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) (2016)

DOI: 10.1109/BIBE.2016.48

Revealing protein-ligand interaction patterns through frequent subgraph mining

Silveira, S. A., Fassio, A. V., da Silveira, C. H., & de Melo-Minardi, R. C.
Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP) (2015)

ADVISe: Visualizing the dynamics of enzyme annotations in UniProt/Swiss-Prot

Silveira, S. A., Rodrigues, A. O., de Melo-Minardi, R. C., da Silveira, C. H., & Meira, W.
IEEE Symposium on Biological Data Visualization (BioVis) (2012)

DOI: 10.1109/BioVis.2012.6378592