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