Ramachandran plot on the web
نویسندگان
چکیده
A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis output. This software is incorporated with all the protein structures available in the Protein Databank.
منابع مشابه
Molecular Modeling and Docking Studies on the First Chlorotoxin-Like Peptide from Iranian Scorpion Mesobuthuseupeus (Meict) and SNP Variants of Matrix Methaloproteinase-2 (MMP-2)
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The main-chain conformations of 237 384 amino acids in 1042 protein subunits from the PDB were analyzed with Ramachandran plots. The populated areas of the empirical Ramachandran plot differed markedly from the classical plot in all regions. All amino acids in alpha-helices are found within a very narrow range of phi, psi angles. As many as 40% of all amino acids are found in this most populate...
متن کاملAn exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)
The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom-the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a ...
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Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as α-helices and β-sheets. Secondary structure is characterized by the local rotational state of the protein backbone, quantified by two dihedral angles called ϕ and ψ. Particular types of secondary structure can generally be described by a single (diffuse) location on a two-dimensional...
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MOTIVATION Statistical methods that compare observed and expected distributions of experimental observables provide powerful tools for the quality control of protein structures. The distribution of backbone dihedral angles ('Ramachandran plot') has often been used for such quality control, but without a firm statistical foundation. RESULTS A new and-simple method is presented for judging the ...
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ورودعنوان ژورنال:
- Bioinformatics
دوره 18 11 شماره
صفحات -
تاریخ انتشار 2002