Ramachandran Plot on The Web (2.0)

Abstract

The Ramachandran plot displays the main chain conformation angles (Phi and Psi) of the polypeptide chain of a protein molecule. The paper reports the updated version of the Ramachandran plot web server and has several improved options for displaying the conformation angles in various regions. In addition, options are provided to display the conformation angles in various secondary structural elements and regions within the user specified Phi and Psi values in the plot. The updated version is accessible at the following URL: http://dicsoft1.physics.iisc.ernet.in/rp/.

Half a century of Ramachandran plots

“…One of them (http:// dicsoft1.physics.iisc.ernet.in/rp/) allows numerous possibilities to analyze specific features of the Ramachandran plot (different types of amino acids, sequence-dependent windows, different regions of the map etc. ; Sheik et al, 2002;Gopalakrishnan, Sowmiya et al, 2007). RAMPAGE is another well designed program from the CCP4 software suite (Winn et al, 2011) that can be found at http://mordred.bioc.cam.ac.uk/ rapper/rampage.php, for example.…”

Substrate-Binding Site of Family 11 Xylanase fromBacillus firmusK-1 by Molecular Docking

“…32) To validate the modeled structure of Xyn11A, a Ramachandran plot of Xyn11A and template were drawn by the Procheck program. 20) The spot distribution in the Ramachandran plot of the Xyn11A structure was similar to the X-ray structure of the B. circulans xylanase. The results showed that the homology-modeled structure of Xyn11A is reasonable and acceptable.…”

“…Validation of the model was carried out using Ramachandran plot calculations computed with the Procheck program. 20) Molecular docking. Xylooligosaccharides preparation.…”

Molecular insights into the binding affinity and specificity of the hemagglutinin cleavage loop from four highly pathogenic H5N1 isolates towards the proprotein convertase furin

“…The result of the amino acid sequence alignment revealed that the H5Sq1 loop has a 50% similarity relative to its template. Then, the geometry and stereochemistry of the loop were validated using Ramachandran plot 2.0 program [23,24]. Of the ten residues of the cleavage loop, nine are located in the fully allowed regions and the other one in the additionally allowed regions of the plot, indicating that the initial structure of the H5Sq1 loop is reasonable.…”