Christoph: /* External links */

2012-07-13T02:10:38Z

‎External links

Christoph: /* External links */

2012-07-13T01:35:49Z

‎External links

Christoph: New page: '''Homology modeling''', also known as '''comparative modeling''' of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and...

2012-07-13T00:47:01Z

New page: '''Homology modeling''', also known as '''comparative modeling''' of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and...

New page

'''Homology modeling''', also known as '''comparative modeling''' of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "''template''"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.<ref name="LeskChothia">Chothia, C; Lesk, AM (1986). "The relation between the divergence of sequence and structure in proteins". ''EMBO J'' '''5''' (4): 823–6. PMC 1166865. PMID 3709526.</ref>

==Popular Web servers for remote homology/fold recognition==
<div style="float:left; margin:0px 0px 0px 0px;">
{| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
|-
! colspan="4" bgcolor="#EFEFEF" | '''Homology modeling servers'''
|-align="center" bgcolor="#1188ee"
!Server name
!Consensus/<br/>single
!Model building/<br/>confidence measure
!FR/<br/>''ab initio''
|-
| [http://www.imperial.ac.uk/phyre/ Phyre] || Single || Model + confidence || FR
|--bgcolor="#eeeeee"
| [http://zhang.bioinformatics.ku.edu/I-TASSER/ I-TASSER] || Single || Model + confidence || FR + ''ab initio''
|-
| [http://www.soe.ucsc.edu/compbio/SAM_T06/T06-query.html SAM-T06] || Single || Model + confidence || FR
|--bgcolor="#eeeeee"
| [http://toolkit.tuebingen.mpg.de/hhpred HHpred] || Single || Confidence || FR
|-
| [http://bioinf.cs.ucl.ac.uk/psipred/psiform.html GenThreader] || Single || ''P''-value || FR
|--bgcolor="#eeeeee"
| [http://pcons.net/ PCONS] || Consensus || Model + ''P''<sub>cons</sub> score || FR
|-
| [http://meta.bioinfo.pl Bioinfo] || Consensus || Model + ''E''-value || FR
|--bgcolor="#eeeeee"
| [http://ffas.ljcrf.edu FFAS] || Single || FFAS score || FR
|-
| [http://robetta.bakerlab.org/ Robetta] || Single || Model + confidence || FR + ''ab initio''
|--bgcolor="#eeeeee"
| [http://sparks.informatics.iupui.edu/SP4/ SP4] || Single || Model + ''Z''-score || FR
|}
<div align="center">"Consensus" indicates that the server collates results from multiple independent servers to form a final prediction, whereas "single" indicates that a server uses only its own local methods. The Model building/confidence measure column indicates whether a server provides as output 3D coordinates of a potential model ("Model") and a score indicating the confidence in the model (Z-score, P-value, E-value and so on). The "FR/ab initio" column indicates whether the server can produce results based only on remote homology/fold recognition ("FR") or can additionally build models in the absence of a template ("ab initio").<ref>Kelley LA, Sternber MJE (2009). "Protein structure prediction on the Web: a case study using the Phyre server". ''Nature Protocols'' '''4''': 363-371. {{doi|10.1038/nprot.2009.2}}</ref>
</div>
</div>

==See also==
*[[wikipedia:Category:Molecular modelling software]]
*[[wikipedia:Homology modeling]]
*[[WHAT IF]]
*[http://biskit.pasteur.fr/ Biskit] — written in [[Python]]
*[http://noch.sourceforge.net/ NOCH] (or NOC)
*[[Jmol]]
*[[PyMOL]]
*[[RasMol]]

==References==
<references/>

==External links==
* [http://www.tcoffee.org/Projects/expresso/index.html 3D-Coffee and Expresso] — a special mode of T-Coffee that uses structural information
* [http://swissmodel.expasy.org//SWISS-MODEL.html SWISS-MODEL] - automated model construction server
* [http://bmm.cancerresearchuk.org/~3djigsaw/ 3D-JIGSAW] - automated model construction server
* [http://www.sbg.bio.ic.ac.uk/~phyre PHYRE] – automated model construction server, replace 3D-PSSM.
* [http://www.salilab.org/modeller/ MODELLER] – widely used standalone program using the spatial restraints method
* [http://modbase.compbio.ucsf.edu/modbase-cgi-new/search_form.cgi ModBase] – database for homology models
* [http://bioinfo.pl/meta/livebench.pl LiveBench] – continuous benchmark for automated prediction servers
* [http://cubic.bioc.columbia.edu/eva/doc/concept.html EVA] – continuous benchmark for automated prediction servers
* [http://structure.bu.edu/cgi-bin/consensus/consensus.cgi Consensus] – Alignment of a sequence (target) to its closest homolog in PDB (template) using a consensus of other alignment methods
* [http://dunbrack.fccc.edu/molide/ MolIDE] – Open-source cross-platform graphical environment for homology modeling
* [http://swift.cmbi.ru.nl/ WHAT IF] – free servers for structure and model analysis, validation, and visualisation.
* [http://swift.cmbi.ru.nl/gv/pdbreport/ PDBREPORT] – lists of errors in PDB files.
* [http://swift.cmbi.ru.nl/gv/whatcheck/ WHAT_CHECK] – downloadable software for structure and model validation.
* [http://supfam.org/SUPERFAMILY/ SUPERFAMILY] – Hidden Markov model library offering remote homology detection at the Structural_Classification_of_Proteins (SCOP)

[[Category:Bioinformatics]]
[[Category:Crystallography]]

@@ Line 65: / Line 65: @@
 * [http://supfam.org/SUPERFAMILY/ SUPERFAMILY] – Hidden Markov model library offering remote homology detection at the Structural_Classification_of_Proteins (SCOP)
 * [http://tardis.nibio.go.jp/homstrad/ HOMSTRAD] (Homologous Structure Alignment Database) &mdash; a curated database of structure-based alignments for homologous protein families.
 [[Category:Bioinformatics]]
 [[Category:Crystallography]]

Homology modeling - Revision history

Christoph: /* External links */

Christoph: /* External links */

Christoph: New page: '''Homology modeling''', also known as '''comparative modeling''' of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and...