This article is part of the supplement: Proceedings of the 6th International Conference of the Brazilian Association for Bioinformatics and Computational Biology (X-meeting 2010)

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Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns

Douglas EV Pires1,2*, Raquel C de Melo-Minardi2, Marcos A dos Santos2, Carlos H da Silveira3, Marcelo M Santoro1 and Wagner Meira2

1 Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil

2 Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil

3 Advanced Campus at Itabira, Universidade Federal de Itajubá, Itabira, 37500-903, Brazil

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BMC Genomics 2011, 12(Suppl 4):S12 doi:10.1186/1471-2164-12-S4-S12

Published: 22 December 2011

Additional files

Additional file 1:

Additional figures and tables. Figure S1 - Performance metrics across EC classes. Figure S2 - Correlation between precision and minimum number of representatives. Figure S3 - The influence of Cα and Cβ distances in the performance. Figure S4 - Feature vector density distribution for proteins of different SCOP classes. Table S1 - Function prediction performance using naive Bayes for gold-standard dataset. Table S2 - Function prediction performance using random forest for the gold-standard dataset.

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Additional 2:

Enzyme gold-standard dataset. List of PDB identifiers that compose the enzyme gold-standard dataset and its family and superfamily assignments.

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