Analysis of structures from Protein Data Bank using atom displacement parameters

Research article: Analysis of structures from Protein Data Bank using atom displacement parameters

Author:  R.C. Masmaliyeva

Institute of Molecular Biology and Biotechnologies, Azerbaijan National Academy of Sciences,

Baku, Azerbaijan

Abstract: Currently there are more than 156,000 macromolecular structures in Protein Data Bank (PDB). If at first times of development of Structural biology the priority purpose was solving as many structures as possible, currently the main purpose is solving structures, which allow understanding different biological processes. This is why validation and refinement of macromolecular structures become more and more important. New validation tools need to be developed. Classic methods of validation are based on physical and chem-ical features of macromolecules, as well as the geometry of amino acids. In our researches, we describe a method of validation by using Atom Displacement Parameters (ADP). ADP illustrates the variation of atom from its main position. Development of the method of statistical analysis of ADP distribution may be used as an effective validation tool. This contribution is devoted to application of statistical analysis of ADPs to PDB and possible use of this method for macromolecular validation.

Keywords: Atom displacement parameters, macromolecular refinement, validation 

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