3. RAMPAGE software is
utilized to analyze
Ramachandran Plot for
protein model evaluation
to examine the regions
where the desired amino
acids are present.
Introduction
4. “ RAMPAGE: Ramachandran Plot
Assessment based on Ramachandran
plot algorithm and Phi-Psi angle
calculations.”
5. Objectives
Available on
RAM0AGE is an online
web based tool that is
publicly available for
the users.
Research
Outcome
Ramachandran plot
algorithm to determine
in which region of the
plot, amino acid
residues lie.
Analyzes
Evaluates the protein
structure, either
predicted model using
any computational tool
for protein 3D structure
prediction.
6. Input
--pdb filename
The server requires
(Compulsory) input
pdb file name.
--rampage-
postscript filename
RAMPAGE results in
output postscript
file name.
Output
Input & Output
7. Regions
Plot defines three
regions: allowed
regions, outliers, and
favored regions.
Evaluation
RAMPAGE is utilized for
protein model evaluation
among known
structures.
Plot
Ramachandran
diagram plots phi
versus psi dihedral
angles for each
residue
Residues
provides the
information about the
residues in the defines
regions.
Validation
Structure validation
tool for the assessment
of the Ramachandran
Plot
Methodology
Analysis
Analysis of protein
model to determine
the regions of desired
amino acids.
8. Here, you can
visualize how
RAMPAGE evaluate
the residues in the
model of target
protein.
Ramachandran Plot
produced by
RAMPAGE represents
the specific residues
in favoured region,
allowed and outlier
region.
9. Regions Ideal Values of Residues
1st Favoured
Region
>=90%
2nd Allowed
Region
>=90%
3rd Outlier Region >=1-2%
Results Analysis
10. RAMPAGE is an offshoot of
RAPPER which generates a
Ramachandran plot using
protein models derived by
protein 3D structure
prediction computational
tools.
Conclusion
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