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Table 4 List of web servers for modeling the protein structure by threading or fold recognition
method along with the webpage URL and the description of programme
S. no.
Name of the web server/group [URL]
Description of the web server/group
1
I-TASSER (Zhang et al. 2005 )[ http://
zhanglab.ccmb.med.umich.edu/I-
TASSER/ ]
3D models are built based on multiple-
threading alignments by LOMETS and
iterative template fragment assembly
SPARKS X (Yang et al. 2011 )[ http://
sparks-lab.org/yueyang/server/
SPARKS-X/ ]
2
This server employs signi cantly
improved secondary structure predic-
tion, real value torsion angle prediction
and solvent accessibility prediction to
model a more accurate protein structure
3
LOOPP (Teodorescu et al. 2004 )[ http://
cbsuapps.tc.cornell.edu/loopp.aspx ]
A fold recognition program based on the
collection of numerous signals to build
the target structure
4
PROSPECT (Xu and Xu 2000 )[ http://
compbio.ornl.gov/structure/prospect ]
PROSPECT is based on scoring func-
tion, which consists of four additive
terms: (i) a mutation term, (ii) a single-
ton fitness term, (iii) a pairwise-contact
potential term, and (iv) alignment gap
penalties
5
MUSTER (Wu and Zhang 2008 )[ http://
zhanglab.ccmb.med.umich.edu/
MUSTER/ ]
Muster generates sequence-template
alignments by combining sequence
prole-prole alignment with multiple
structural information
6
PHYRE2 (Kelley and Sternberg 2009 )
[ http://www.sbg.bio.ic.ac.uk/ * phyre2/
html/page.cgi?id=index ]
A server which uses pro le - pro le
matching algorithms to build the protein
model
(a) Detectable similarity (Greater than or equal to 30 %) between the target
sequence and the template structures and
(b) Availability of a correct alignment between them.
Homology or Comparative modeling is a multistep process that can be sum-
marized in following six steps:
3.3.1 Template Search, Selection and Alignment
Template search is generally done by comparing the target sequence with the
sequence of each of the structures in the PDB database. The performance depends
on the sensitivity of the comparison of target and template sequences by various
programmes e.g. FASTA which is available at http://www.ebi.ac.uk/Tools/sss/fasta/
while, BLAST and PSI-BLAST (Altschul et al. 1997 ) are available at http://blast.
ncbi.nlm.nih.gov/Blast.cgi . The simplest template selection rule is to select the
structure with the highest sequence similarity with the target sequence. The quality
of a template increases with its overall sequence similarity with the target and
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