PRODIV-TMHMM

By | September 22, 2011

The PRODIV-TMHMM webserver actually consists of four separate topology predictors.
PRODIV-TMHMM, PRO-TMHMM and S-TMHMM are hidden Markov model based servers for topology prediction of transmembrane proteins. Details of the programs are described in:

Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information, Håkan Viklund and Arne Elofsson, Protein Science Vol. Protein Sci. 2004 Jul;13(7):1908-17

TOP-MOD uses the output from PRODIV-TMHMM and predicts reentrant regions (membrane dipping loops) in the predicted loop regions. TOP-MOD is based on observed differences in amino acid composition between reentrant regions and loops in general. Details are described in:

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes, Håkan Viklund, Erik Granseth and Arne Elofsson, J. Mol. Biol. 2006 Aug 18;361(3):591-603

PRODIV-TMHMM, PRO-TMHMM and S-TMHMM provide three-state topology predictions for each residue of the sequence: membrane (M), inside (i) and outside (o). TOP-MOD predicts each residue to be either membrane (M), inside loop (l), inside reentrant regions (r), outside loop (L) or outside reentrant region (R). The orientation with respect to the different types of membranes is defined as follows:

Plasma membrane: inside – cytoplasmic, outside – extracellular
Endoplasmic reticulum, Golgi, nuclear, peroxisome, endosome, vacuole, and vesicle membranes: inside – cytoplasmic, outside – luminal
Inner bacterial membrane: inside – cytoplasmic, outside – periplasmic or extracellular
Outer bacterial membrane: inside – periplasmic, outside – extracellular
Inner mitochondrial or chloroplast membrane: inside – matrix/stroma, outside – intermembrane space
Outer mitochondrial or chloroplast membrane: inside – cytoplasmic, outside – intermembrane space
Chloroplast thylakoid membrane: inside – stromal, outside – thylakoid space

Name
PRODIV-TMHMM
Documentation
http://www.pdc.kth.se/~hakanv/prodiv-tmhmm/about.html
Protocol
SOAP
WSDL
Endpoint
http://wsdl.sbc.su.se/cgi-bin/prodivtmhmm.cgi
Topic
Biology
Type
Tags
, , , ,
Description

The PRODIV-TMHMM webserver actually consists of four separate topology predictors. PRODIV-TMHMM, PRO-TMHMM and S-TMHMM are hidden Markov model based servers [...]

Further information

The PRODIV-TMHMM webserver actually consists of four separate topology predictors.
PRODIV-TMHMM, PRO-TMHMM and S-TMHMM are hidden Markov model based servers for topology prediction of transmembrane proteins. Details of the programs are described in:

Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information, Håkan Viklund and Arne Elofsson, Protein Science Vol. Protein Sci. 2004 Jul;13(7):1908-17

TOP-MOD uses the output from PRODIV-TMHMM and predicts reentrant regions (membrane dipping loops) in the predicted loop regions. TOP-MOD is based on observed differences in amino acid composition between reentrant regions and loops in general. Details are described in:

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes, Håkan Viklund, Erik Granseth and Arne Elofsson, J. Mol. Biol. 2006 Aug 18;361(3):591-603

PRODIV-TMHMM, PRO-TMHMM and S-TMHMM provide three-state topology predictions for each residue of the sequence: membrane (M), inside (i) and outside (o). TOP-MOD predicts each residue to be either membrane (M), inside loop (l), inside reentrant regions (r), outside loop (L) or outside reentrant region (R). The orientation with respect to the different types of membranes is defined as follows:

Plasma membrane: inside – cytoplasmic, outside – extracellular
Endoplasmic reticulum, Golgi, nuclear, peroxisome, endosome, vacuole, and vesicle membranes: inside – cytoplasmic, outside – luminal
Inner bacterial membrane: inside – cytoplasmic, outside – periplasmic or extracellular
Outer bacterial membrane: inside – periplasmic, outside – extracellular
Inner mitochondrial or chloroplast membrane: inside – matrix/stroma, outside – intermembrane space
Outer mitochondrial or chloroplast membrane: inside – cytoplasmic, outside – intermembrane space
Chloroplast thylakoid membrane: inside – stromal, outside – thylakoid space

Original source
BioCatalogue

Leave Your Comment

Your email will not be published or shared. Required fields are marked *

*

*

You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>