Secondary and Tertiary Structure Prediction of Proteins: A Bioinformatic Approach - Complex System Modelling and Control Through Intelligent Soft Computations - page 545

Table 5 List of web servers for protein structure quality validation along with the webpage URL
and the programme description
S. no. Name of the web server/group [URL] Description of the web server/group

1 QMEAN (Benkert et al. 2009 )[ http://

swissmodel.expasy.org/qmean/cgi/
index.cgi ]

Quality estimate is based on geometrical
analysis of single model, and the clus-
tering-based scoring function

2 PROSA-WEB (Wiederstein and Sippl

2007 )[ https://prosa.services.came.sbg.
ac.at/prosa.php ]

Quality is checked by generation of
Z-scores and energy plots that highlight
potential problems spotted in protein
structures

3 PROCHECK (Laskowski et al. 1993 )

[ http://services.mbi.ucla.edu/SAVES/ ]

Stereo chemical quality of a protein
structure is checked by analyzing resi-
due-by-residue geometry and overall
structural geometry

4 VERIFY-3D (Bowie et al. 1991 ; Luthy

et al. 1992 )[ http://services.mbi.ucla.
edu/SAVES/ ]

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

5 ERRAT (Colovos and Yeates 1993 )

[ http://services.mbi.ucla.edu/SAVES/ ]

This server analyzes the statistics of
non-bonded interactions between differ-
ent atom types and plots the value of the
error function

3.3.6 Homology Models Repositories

However, there are many repositories available, which contain protein homology
models generated using various automated methods that provide models which
serve as starting points for biologists/experimentalists. SWISS-MODEL repository
( http://swissmodel.expasy.org/repository/ ) is one of the databases of annotated
three-dimensional comparative protein structure models generated by the fully
automated homology-modelling pipeline SWISS-MODEL. Protein Model Portal
( http://proteinmodelportal.org ) is another repository aimed at storing manually built
3D models of proteins (Arnold et al. 2009 ). The most recent database is Modbase
( http://modbase.compbio.ucsf.edu ) which contains the datasets of comparative
protein structure models, calculated by modeling pipeline ModPipe (Pieper et al.
2011 ).
Several additional features when clubbed to the methods for tertiary structure
prediction generate hybrid methods which are used to produce more accurate
protein tertiary structures. Following section discusses about these hybrid methods
for the protein tertiary structure prediction.