Secondary and Tertiary Structure Prediction of Proteins: A Bioinformatic Approach - Complex System Modelling and Control Through Intelligent Soft Computations - page 549

Table 7 List of meta-servers for protein tertiary structure prediction along with the webpage URL
and the description of the programs
S. no. Name of the web server/group [URL] Description of the web server/group

1 LOMETS (Wu and Zhang 2007 )

[ http://zhanglab.ccmb.med.umich.
edu/LOMETS/ ]

Meta server that includes locally installed
threading programs FUGUE, HHpred,
SPARKS. LOMETS generates the nal
models using a consensus approach

2 3D-Jury (Ginalski et al. 2003 )[ http://

BioInfo.PL/Meta/ ]

The meta server provides access and results
assessment from various remote predictors
including, 3DPSSM, ESyPred3D, FUGUE,
HHpred, mGenTHREADER etc.

3 GeneSilico (Kurowski and Bujnicki

2003 )[ https://genesilico.pl/meta2/ ]

The meta server provides access to various
remote and local predictors including
3DPSSM, FUGUE, HHpred, mGenTH-
READER, Pcons, Phyre, etc.

4 Pcons.net (Lundstr m et al. 2001 ),

(Wallner et al. 2007 )[ http://pcons.
net/ ]

ö The Pcons protocol analyzes the set of

protein models and looks for recurring
three-dimensional structural patterns and
assigns a score

5. 3D-SHOTGUN (Fischer 2003 )

[ http://bioinfo.pl/meta ]

This meta-predictor consists of three steps:
(i) assembly of hybrid models, (ii) confi-
dence assignment, and (iii) selection

predictions by LOMETS were at least 7 % more accurate than the best individual
servers. In addition to the 3D structure prediction by threading, LOMETS also
provides highly accurate contact and distance predictions for the query sequences.
The performance of LOMETS can be analyzed by the fact that average CPU time
for a medium size protein ( 200 residues) is less than 20 min when the programs

are run in parallel on nine nodes of the cluster.
A List of Meta-servers for protein tertiary structure prediction along with the
webpage URL and the description of the programs in Table 7 .
The need for critical evaluation of various methods and developments in the

∼

eld

of protein structure prediction is successfully ful lled by CASP meetings. The

following section gives an overview of several agenda of CASP.

6 CASP

Protein structure prediction algorithms are constantly being developed and rede-

fined to reach the experimental accuracy. Therefore, protein structure prediction
strategies and methodologies are tested every 2 years in the Critically Assessment
of techniques for protein Structure Prediction (CASP) meeting, which started since
1994. Since then, ten successful CASP meetings are over by 2012 and CASP11 is
due in 2014. The participation by various research groups in the CASP are