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rampage server for ramachandran plot

by Kailee Turcotte Published 3 years ago Updated 2 years ago

RAMPAGE is an offshoot of RAPPER which generates a Ramachandran plot using data Davis, W.B. ramachandran (PDBStruct) generates the Ramachandran plot for the protein stored in PDBStruct, a MATLAB structure containing PDB-formatted data, such as returned by getpdb or pdbread.

Full Answer

What is a Ramachandran plot?

You can upload a PDB-formatted file to the server and the backbone dihedral angles will be plotted on our accurate Ramachandran Plot Instructions: Select a protein structure file in PDB format from your hard disk. Select Amino Acid type to show. Check the boxes for Glycine, Verbosity, and Labels as desired; Click the GO! button

What is the Ramachandran plot validation server?

After the refinement process, validation of the model was carried out using Ramachandran plot calculations computed with the RAMPAGE Server. The distributions of the Ramachandran plots of non ...

What is Ramachandran server?

03/11/2020 · In biochemistry, a Ramachandran plot, originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. --rampage-postscript filename RAMPAGE revealed that the predicted model has 94% amino …

What is rapper-Ramachandran plots?

The Ramachandran plot for p27 SJ using RAMPAGE software revealed that among the 263 residues, 259 (99.2%) were in favoured region, 2 (0.8%) were in allowed region and 0 (0.0%) were in disallowed ...

How do I run a Ramachandran plot server?

Instructions:Select a protein structure file in PDB format from your hard disk.Select Amino Acid type to show.Check the boxes for Glycine, Verbosity, and Labels as desired.Click the GO! button.

What is rampage in bioinformatics?

DESCRIPTION. RAMPAGE is an offshoot of RAPPER which generates a Ramachandran plot using data derived by the Richardsons and coworkers. ... The Ramachandran diagram plots phi versus psi dihedral angles for each residue in the input pdb file.

What does a Ramachandran plot show?

The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963).

How can I check my Ramachandran plot?

The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in a peptide. In sequence order, φ is the N(i-1),C(i),Ca(i),N(i) torsion angle and ψ is the C(i),Ca(i),N(i),C(i+1) torsion angle. The plot was developed in 1963 by G. N. Ramachandran, et.

What is Rampage software?

DESCRIPTION. RAMPAGE is an offshoot of RAPPER which generates a Ramachandran plot using data derived by the Richardsons and coworkers. It is recommended that it be used for this purpose in preference to PROCHECK, which is based on much older data.

How do you test protein structure?

Specific Structure ChecksStereochemical Validation. All chiral centers of proteins and nucleic acids are checked for correct stereochemistry. ... Atom Nomenclature. ... Close Contacts. ... Ligand and Atom Nomenclature. ... Sequence Comparison. ... Distant Waters. ... Checks against Experimental Data. ... Validation Server.

How many quadrants are present in Ramachandran plot?

Glycine has no side chain and therefore can adopt phi and psi angles in all four quadrants of the Ramachandran plot.

What are outliers in Ramachandran plot?

Ramachandran outliers are those amino acids with non-favorable dihedral angles, and the Ramachandran plot is a powerful tool for making those evident. ... Most of the time, Ramachandran outliers are a consequence of mistakes during the data processing.

How do you find the phi and psi angle?

As with any peptide the conformation of the backbone is determined by the values of two torsional angles. In sequence order, phi (φ) is the C(i-1),N(i),Ca(i),C(i) torsion angle and psi (ψ) is the N(i),Ca(i),C(i),N(i+1) torsion angle.

What is the full name of GN Ramachandran?

Gopalasamudram Narayanan RamachandranGopalasamudram Narayanan Ramachandran, or G.N. Ramachandran, FRS (8 October 1922 – 7 April 2001) was an Indian physicist who was known for his work that led to his creation of the Ramachandran plot for understanding peptide structure. He was the first to propose a triple-helical model for the structure of collagen.

What is Ramachandran plot PDF?

Sasisekharan. Ramachandran plot provides a simple two-dimensional graphic. representation of all possible protein structures in terms of torsion angles. Although the plot was developed using theoretical. methods, mathematical calculations and models building, once the protein structure began to discover, the importance.31-Dec-2018

SYNOPSIS

rapper $CCP4/share/rapper/params.xml rampage --pdb filename --rampage-postscript filename --rapper-dir directoryname#N#[ Keyworded input]

DESCRIPTION

RAMPAGE is an offshoot of RAPPER which generates a Ramachandran plot using data derived by the Richardsons and coworkers. It is recommended that it be used for this purpose in preference to PROCHECK, which is based on much older data.

KEYWORDED INPUT

Name of the directory containing the data library. This should normally be set to $CCP4/user/share.

REFERENCES

S.C. Lovell, I.W. Davis, W.B. Arendall III, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, D.C. Richardson, Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins: Struct. Funct. Genet. 50 437-450 (2003).

AUTHORS

Nicholas Furnham, Paul de Bakker, Mark DePristo, Reshma Shetty, Swanand Gore and Tom Blundell.

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