Search results
Ramachandran plot. Introduction. This server will display a Ramachandran plot, against a background of phi-psi probabilities. Methods. This server will display a coloured Ramachandran plot. Blue means helix, red means strand and green means turn and loop according to DSSP. The lines in the plot indicate prefered areas.
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.
A selection of programs to generate and display Ramachandran (phi/psi) plots for proteins from PDB files.
The Ramachandran plot is probably the very best indicator of the quality of the experimental determination of three dimesional protein coordinates. This server analyses the Ramachandran plot of a PDB file and compares it with the Ramachandran plots of about 400 representative structures solved at high resolution.
RAMPAGE is a consequence of RAPPER which generates a Ramachandran plot by data derivative by the Richardsons and coworkers. RAPPER performs conformer modelling through sampling residue-specific phi / psi propensity tables and rotameric states with given a set of restraints.
Drawing Ramachandran (phi/psi) plots for Proteins with R. These pages shows how to use R to draw a protein backbone's psi/phi torsion angles (ϕ,ψ) from a supplied file as a scatter plot overlayed on a filled contour plot showing the favoured and allowed regions, for example:
3D Macromolecule analysis, includes Kinemage 3D graphics, Rampage for Ramachandran plot generation, MolProbity structure validation, and more
The Ramachandran plot function in the Model Panel plots the distribution of amino acid backbone conformations in peptide and protein structures. It is also implemented as the command ramachandran. See also: RR Distance Maps, Rotamers, Structure Measurements, ksdssp
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...
A special way for plotting and visualization of protein torsion angles was introduced by Ramachandran and co-authors and has since then been called the Ramachandran plot. In the Ramachandran plot, we can view the distribution of torsion angles in a protein structure (image below).
