WHATCHECK

 

WHATCHECK

Aim

To check the steriochemical properties of given protein by WHATCHECK method.

Principle

Homology modeling is rapidly becoming the method of choice for obtaining three dimensional coordinates for proteins because genome projects produce sequences at a much higher rate than NMR and X ray laboratories can solve the three dimensional structures. However , the quality of protein models will not be immediately clear to invoices and support with the evaluation seems to be needed. Expert users are sometimes interested in evaluating the quality of modeling programs rather than the quality of the model themselves.

WHATCHECK has been derived from a subset of protein verification tools from the Whatif program, this does extensive checking of many sterochemical parameters of the residues in the model. The final homology model has to be evaluated to make sure that the structural features of the model are consistent with the physiochemical rules. This involves checking anomalies in ᴪ-ᴪ angles, bond length, close contacts and soon. Another way of checking the quality of a protein model is to implicitly take these steriochemical properties into account. This is a method that detects errors by compiling statistical profiles of spatial features and interaction energy from experimentally determined structures. By comparing the statistical parameters with the constructed model, the method reveals which regions of a square appear to be folded normally and which regions do not. If structural irregularities are found, the region is considered to have errors and has to be further refined. WHATCHECK ia a program that can be used to detect deviations on protein structures, specifically for large scale studies. It can be seen through a web application or as an application or as a standalone software and doesnot need experimental data. The software has been tested on more than 3000  structures from the Brookhaven protein data bank.

 

Procedure

Access https://saves.mbi.ucla.edu/

Click on “ Choose file” and select PDB file

Click on “RUN program”

Click on WHATCHECK start

Click on Results

Click on Red box to know ''error''

Click on Yellow box to know ''warning''

Click on Green box to know ''the score''

 

Result

The steriochemical property of given protein was identified.

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