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ccPDB: compilation and creation of data sets from Protein Data Bank
Harinder Singh1, Jagat Singh Chauhan, M Michael Gromiha
1Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India.
Nucleic Acids Research
|December 6, 2011
Summary
The ccPDB database offers curated protein data sets from scientific literature and the Protein Data Bank (PDB). It enables researchers to create custom data sets for bioinformatics analysis and protein structure annotation.
Area of Science:
- Biochemistry
- Bioinformatics
- Structural Biology
Background:
- Protein Data Bank (PDB) is a crucial resource for structural biology.
- Developing bioinformatics methods requires comprehensive and curated datasets.
- Existing resources may lack flexibility for custom data set generation.
Purpose of the Study:
- To create a comprehensive database of protein data sets.
- To facilitate the development of bioinformatics tools for protein annotation.
- To provide a flexible platform for generating customized protein datasets.
Main Methods:
- Compiled datasets from scientific literature.
- Extracted datasets from the latest Protein Data Bank (PDB) releases.
- Developed a user-friendly, six-step module for creating custom PDB datasets.
- Integrated web services for job submission, structure annotation, and pattern generation.
Main Results:
- ccPDB database established with >30 types of protein datasets.
- Datasets include secondary structure, nucleotide/metal interacting residues, and DNA/RNA binding residues.
- A flexible module allows users to generate tailored datasets from PDB.
Conclusions:
- ccPDB serves as a valuable resource for protein structure and function annotation.
- The database supports the advancement of bioinformatics research through accessible data.
- ccPDB enhances protein data accessibility and customization for researchers.
