Homology model validation

Homology model can be validated in multiple ways.

Here you will find useful description on how to validate your homology model.

Web-servers:

UCLA-DOE LAB — SAVES : The Structure Analysis and Verification Server (New Link)

This metaserver runs 6 programs for checking and validating protein structures during and after model refinement.

PROCHECK : Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry.
WHAT_CHECK : Derived from a subset of protein verification tools from the WHATIF program (Vriend, 1990), this does extensive checking of many sterochemical parameters of the residues in the model.
ERRAT : Analyzes the statistics of non-bonded interactions between different atom types and plots the value of the error function versus position of a 9-residue sliding window, calculated by a comparison with statistics from highly refined structures.
VERIFY_3D : Determines the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigning a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures.
PROVE : Calculates the volumes of atoms in macromolecules using an algorithm which treats the atoms like hard spheres and calculates a statistical Z-score deviation for the model from highly resolved (2.0 Å or better) and refined (R-factor of 0.2 or better) PDB-deposited structures.
CRYST1 record matches : Considers the CRYST1 record and search the entire PDB for matches and report these as possibly similar structures.
Ramachandran Plot : Produce an interactive Ramachandran plot. Also a standalone server linked above.

RAMPAGE : Ramachandran Plot Analysis

ProSA-web : Performs Protein structure analysis

It will give Overall model quality and

Local model quality.

Comments

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Python : Turtle tree

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Plagarism Checker

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