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BioMed Research International
Volume 2014, Article ID 947416, 12 pages
http://dx.doi.org/10.1155/2014/947416
Research Article

iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach

1Computer Department, Jingdezhen Ceramic Institute, Jingdezhen 333046, China
2Information School, ZheJiang Textile & Fashion College, Ningbo 315211, China
3Gordon Life Science Institute, Boston, MA 02478, USA
4Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia

Received 15 February 2014; Revised 26 April 2014; Accepted 29 April 2014; Published 22 May 2014

Academic Editor: Liam McGuffin

Copyright © 2014 Wang-Ren Qiu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

S1: An analysis of the benchmark dataset used in Hu et al. (Biopolymers, 2011, 95, 763-771)

S2: List of self-conflict samples in the benchmark dataset used in Hu et al. (Biopolymers, 2011, 95, 763-771)

S3: Benchmark dataset used for studying the Arg-methylation. It contains 1,481 samples, of which 185 are positive and 1,296 negative. These data were extracted from UniProtKB/Swiss-Prot database (version UniProt release 2013_06).

S4: Benchmark dataset used for studying the Lys-methylation. It contains 1,884 samples, of which 226 are positive and 1,518 negative. These data were extracted from UniProtKB/Swiss-Prot database (version UniProt release 2013_06).

S5: Seven negative subsets for studying Arg-methylation. Each subset contains 185 negative samples randomly taken from the 1,296 negative samples in Online Supporting Information S3 except for the 6th subset, which contains 186 samples. None of the samples in one subset occurs in any other subset.

S6: Seven negative subsets for studying Lys-methylation. Each subset contains 217 negative samples randomly taken from the 1,518 negative samples in Online Supporting Information S4 except for the 5th subset, which only contains 216 samples. None of the samples in one subset occurs in any other subset.

S7: Independent dataset for studying the Arg-methylation. It contains 75 samples, of which 20 are positive and 55 negative. None of the samples listed here occurs in Online Supporting Information S3.

S8: Independent dataset for studying the Lys-methylation. It contains 40 samples, of which 14 are positive and 26 negative. None of the samples listed here occurs in Online Supporting Information S4.

S9: The code for encoding the peptides investigated in this paper.

  1. Supplementary Material