Bioinformatics Tools

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====== secondary structure assignment ======


[[http://www.aber.ac.uk/~phiwww/prof/ | PROF:]]Secondary Structure Prediction System

[[http://www.compbio.dundee.ac.uk/www-jpred/ | Jpred:]] A Secondary Structure Prediction Server

[[http://scratch.proteomics.ics.uci.edu | SSpro 4.0 Server:]] Protein Secondary Structure Prediction with Homology Analysis 

[[http://bioinf.cs.ucl.ac.uk/psipred/ | The PSIPRED protein structure prediction server:]] You may select one of three prediction methods to apply to your sequence: PSIPRED - a highly accurate method for protein secondary structure prediction, MEMSAT - our widely used transmembrane topology prediction method and GenTHREADER - a sequence profile based fold recognition method.


[[http://webclu.bio.wzw.tum.de/stride/ | Stride Web Interface:]] Protein secondary structure assignment

[[http://genamics.com/expression/strucpred.htm| Genamics Expression software:]] Predicting the Secondary Structure of Your Protein: xpression provides an interface to a large range of sophisticated secondary structure prediction algorithms. This section provides an introduction to the interface and a brief overview of the different algorithms.


[[http://compbio.soe.ucsc.edu/HMM-apps/HMM-applications.html | SAM-T08:]] protein structure prediction, tested in **CASP8**.


[[http://www.predictprotein.org|PredictProtein]] - Structure Prediction and Sequence Analysis:motif search , domain search, alignment, disulphide bridge find, predicted secondary structure , predicted protein-protein interaction sites, prediction of DNA binding residues from sequence, protein sequence analysis, protein function prediction.


[[http://bioweb.pasteur.fr/seqanal/interfaces/dssp-simple.html | DSSP:]] Definition of secondary structure of proteins given a set of 3D coordinates


[[http://swift.cmbi.ru.nl/gv/dssp/| DSSP:]]The DSSP program was designed to standardize secondary structure assignment. DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). DSSP is also the program that calculates DSSP entries from PDB entries. DSSP does not predict secondary structure. 

====== other tools ======

[[http://www.ebi.ac.uk/InterProScan/ | InterProScan:]] InterPro is a database of protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences

[[http://munk.csse.unimelb.edu.au/pro-origami/ | Pro-Origami:]]Pro-origami is a system for automatically generating protein structure cartoons. The cartoons are intended to make protein structure easy to interpret by laying out the secondary and super-secondary structure in two dimensions in a manner that makes the structure clear.


====== CASP8 ======


[[http://www.sbg.bio.ic.ac.uk/~phyre/html/casp8.html |  Results:]] scores in CASP8 competition.
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