Ramachandran plot


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Ram·a·chan·dran plot

(rahm'a-chahn'drahn),
a graphic representation in which the dihedral angle of rotation about the α-carbon-to-carbonyl-carbon bond in polypeptides is plotted against the dihedral angle of rotation about the α-carbon-to-nitrogen bond.
Synonym(s): conformational map
[G. N. Ramachandran]
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References in periodicals archive ?
The 3D protein structures were validated using RAMPAGE Ramachandran plot and functional structures were predicted based on the homologous regions from other species including human, rat, mouse and panda.
PREDICTION OF OGG1 STRUCTURAL AND FUNCTIONAL MOTIFS WITH ACTIVE BINDING SITES FROM CAMELUS DROMEDARIES
Rampage server was used for the validation of 3d structure modeled by plotting Ramachandran plot (Ramachandran GN, et al.
Identification of Upregulated Nitrogen Fixing Bacteria for Arachis hypogaea by Exploring Natural Combination: A Physical, Biochemical, and In silico Approach
Ramachandran Plot generated by RAMPAGE (http://mordred.bioc.cam.ac.uk) further vali-dated the modelled protein.
Novel Recombinant Traceable c-Met Antagonist-Avimer Antibody Mimetic Obtained by Bacterial Expression Analysis
The modelled protein has to be validated and it is done by online server RAMPAGE (Ramachandran Plot Analysis) based on an assessment of Ramachandran Plot.
Structural Prediction and Mutational Analysis of Rv3906c Gene of Mycobacterium tuberculosis [H.sub.37] Rv to Determine Its Essentiality in Survival
The model deriving from the SWISS-MODEL had energy and steric values raging between the values recorded for the other two mentioned strategies; therefore, the model resulting from MODELLER due to the adoption of the restriction method allowed the best steric evaluation results: 96.4% of the residues in favorable regions of the Ramachandran plot. The global MODELLER measurement was also satisfactory, this model recorded normalized discrete optimized protein energy (zDOPE) score (-1.94), and it indicated that the atom pair distances in the model comply the distances recorded for a large sample of known protein structures; therefore, it was the model of choice (Table 1).
Identification of Lutzomyia longipalpis Odorant Binding Protein Modulators by Comparative Modeling, Hierarchical Virtual Screening, and Molecular Dynamics
To validate the backbone conformation of the predicted structure, the Phi/Psi Ramachandran plot was obtained through PROCHECK server (Laskowski et al., 2001).
OsDOF18, a DOF transcription factor from rice confers abiotic stress tolerance in Escherichia coli
Ramachandran plot for the normal pRB showed 91.7% residues in the favorable regions.
In Silico Analysis of Missense Substitutions in RB1 Gene and Their Effect on Metabolic Pathways
The reliability of predicted 3D structures of all the proteins of waxy genes were checked using Ramachandran plot. Ramachandran plots were finally obtained as homology model and template for quality assessment of 3D model.
Homology Modeling, Functional Annotation and Comparative Genome Analysis of GBSS Enzyme in Rice and Maize Genomes
The backbone conformation of the refined model was validated using Ramachandran plot obtained through PROCHECK.
Discovery of novel inhibitors for nek6 protein through homology model assisted structure based virtual screening and molecular docking approaches
Validation was performed by evaluating the stereochemical feasibility of the torsion angles using the Ramachandran Plot (RP), (14) generated using the graphic package Ramachandran Plot (version 2) hosted on Indian Institute of Science, Bangalore server.
Mutation in the PCSK9 gene in Omani Arab subjects with autosomal dominant hypercholesterolemia and its effect on PCSK9 protein structure
All the predicted protein structures were passed through quality analysis and structural validation by Ramachandran plot assessment.
In-silico Analysis of Loop Residues of the Receptor Binding Domain of Bacillus thuringiensis Cry2Ac11 Toxin
PROCHECK analysis of the model for T1 exposed that, at resolution 3.52 [Angstrom] and R-factor of0.239, Psi-Phi pairs in Ramachandran plot (Fig.
Campylobacter jejuni ATCC 700819: an in silico approach to identify and categorize probable drug targets by subtractive genome analysis

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