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Applications of complementarity plot in error detection and structure validation of proteins

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Title Applications of complementarity plot in error detection and structure validation of proteins
 
Creator Basu, Sankar
Bhattacharyya, Dhananjay
Banerjee, Rahul
 
Subject Complementarity
Packing and electrostatics
Structure validation
 
Description 188-200
The complementarity
plot (CP) is based on packing and electrostatics of amino acid residues buried
within globular proteins and is a sensitive indicator of the harmony or
disharmony of interior residues with regard to short and long range forces
sustaining the native fold. As a structure validation tool, it has already been
reported to be effective in detecting erroneous side-chain torsions in
obsoleted structures. The current study describes the design of several local
and global scores based on CP and surveys their utilities in discriminating
between obsolete structures and their corresponding upgraded counterparts,
detection of wrong rotamer assignments and in identifying packing anomalies.
CPs are especially effective in the detection of low-intensity errors (in
main-chain geometrical parameters) diffused over the entire polypeptide chain.
The methodology is also used to confirm the integral role played by strategic
deviations (in main-chain geometrical parameters) in maintaining fold
integrity, as reversal to their corresponding ideal values (either unimodal or
conformation dependent) lead to large-scale structural distortions. A special
feature of this validation tool is to signal unbalanced
partial charges within protein interiors. The application of CP in protein
homology modeling and protein design is
also demonstrated.
 
Date 2014-07-14T05:48:56Z
2014-07-14T05:48:56Z
2014-06
 
Type Article
 
Identifier 0975-0959 (Online); 0301-1208 (Print)
http://hdl.handle.net/123456789/29083
 
Language en_US
 
Rights CC Attribution-Noncommercial-No Derivative Works 2.5 India
 
Publisher NISCAIR-CSIR, India
 
Source IJBB Vol.51(3) [June 2014]