CMD

A database to store the bonding states of cysteine motifs with secondary structures

Hamed Bostan, Naomie Salim, Zeti Azura Mohamed Hussein, Peter Klappa, Mohd Shahir Shamsir

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD) is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

Original languageEnglish
Article number849830
JournalAdvances in Bioinformatics
Volume2012
DOIs
Publication statusPublished - 2012

Fingerprint

Cysteine
Databases
Disulfides
Application programming interfaces (API)
Redundancy
Amino acids
Screening
Amino Acid Motifs
Throughput
Proteins
Amino Acid Sequence
Software
Chemical analysis
Amino Acids

ASJC Scopus subject areas

  • Computer Science Applications
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Biomedical Engineering

Cite this

CMD : A database to store the bonding states of cysteine motifs with secondary structures. / Bostan, Hamed; Salim, Naomie; Mohamed Hussein, Zeti Azura; Klappa, Peter; Shamsir, Mohd Shahir.

In: Advances in Bioinformatics, Vol. 2012, 849830, 2012.

Research output: Contribution to journalArticle

Bostan, Hamed ; Salim, Naomie ; Mohamed Hussein, Zeti Azura ; Klappa, Peter ; Shamsir, Mohd Shahir. / CMD : A database to store the bonding states of cysteine motifs with secondary structures. In: Advances in Bioinformatics. 2012 ; Vol. 2012.
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