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- Title
Mining the Protein Data Bank to Differentiate Error from Structural Variation in Clustered Static Structures: An Examination of HIV Protease.
- Authors
Venkatakrishnan, Balasubramanian; Palii, Miorel-Lucian; Agbandje-McKenna, Mavis; McKenna, Robert
- Abstract
The Protein Data Bank (PDB) contains over 71,000 structures. Extensively studied proteins have hundreds of submissions available, including mutations, different complexes, and space groups, allowing for application of data-mining algorithms to analyze an array of static structures and gain insight about a protein's structural variation and possibly its dynamics. This investigation is a case study of HIV protease (PR) using in-house algorithms for data mining and structure superposition through generalized formulæ that account for multiple conformations and fractional occupancies. Temperature factors (B-factors) are compared with spatial displacement from the mean structure over the entire study set and separately over bound and ligand-free structures, to assess the significance of structural deviation in a statistical context. Space group differences are also examined.
- Subjects
HIV; PROTEIN structure; PROTEOLYTIC enzymes; GENETIC mutation; DATA mining
- Publication
Viruses (1999-4915), 2012, Vol 4, Issue 3, p348
- ISSN
1999-4915
- Publication type
Case Study
- DOI
10.3390/v4030348