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PRTAD


NAR Molecular Biology Database Collection entry number 1176
Sun X.1, Di Wu2, Jernigan R.1,3, Wu Z.1,4
1Program on Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa 50011, USA
2Department of Mathematics, Western Kentucky University, Bowling Green, Kentucky 42101, USA
3Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
4Department of Mathematics, Iowa State University, Ames, Iowa 50011, USA

Database Description

PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modeling. The database is developed to host and analyze the statistical data for protein residue level "virtual" bond and torsion angles, based on their distributions in databases of known protein structures such as in the PDB Data Bank. PRTAD is capable of generating, caching, and displaying the statistical distributions of the angles of various types. The collected information can be used to extract geometric restraints or define statistical potentials for protein structure determination. PRTAD is supported with a friendly designed web interface so that users can easily specify the angle types, and retrieve, visualize, or download the distributions of the angles as they desire. PRTAD is freely accessible at http://www.math.iastate.edu/prtad.

Acknowledgements

The work is partially supported by the research funds provided by the Department of Mathematics, the Graduate Program on Bioinformatics and Computational Biology, and the Lawrence Baker Center for Bioinformatics and Biological Statistics at Iowa State University, the New Faculty Startup Fund provided by the Ogden College of Science and Engineering of Western Kentucky University, and the NIH/NIGMS grant R01GM081680.

References

1. Wu, D., Cui, F., Jernigan, R., and Wu, Z. (2007) PIDD: Database for Protein Inter-Atomic Distance Distributions. Nucleic Acids Res. 35 (Database issue): D202-D207
2. Feng, Y., Kloczkowski, A., Jernigan, R. (2007) Four-body contact potentials derived from two protein databases to discriminate native structures from decoys, Proteins: Struct. Funct. Bioinf. 68(1): 57-66

Subcategory: Protein properties
Subcategory: Protein structure

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