Bioinformatics Links Directory : Biochemical Features

The resources in this section include protein identification tools as well as tools which can give you information on the chemical structures and amino acid properties of peptide sequences.

NRSAS - (Found June 19, 2008 )

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.
http://www.receptors.org/NR/servers/html/

CBS DAS protein viewer - (Found June 19, 2008 )

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.
http://www.cbs.dtu.dk/cgi-bin/das

CUPSAT - (Found June 19, 2008 )

Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.
http://cupsat.uni-koeln.de/

CysView - (Found June 19, 2008 )

CysView takes as input various annotated formats of protein sequences, and graphically displays cysteine pairing patterns. It also groups proteins with similar disulfide connectivity patterns.
http://research.i2r.a-star.edu.sg/CysView/

DiANNA - (Found June 19, 2008 )

DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.
http://bioinformatics.bc.edu/clotelab/DiANNA/

DISULFIND - (Found June 19, 2008 )

DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.
http://disulfind.dsi.unifi.it/

eBioinformatics - (Found June 19, 2008 )

This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.
http://www.ebioinformatics.org/

EMBOSS - (Found June 19, 2008 )

Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.
http://cbrmain.cbr.nrc.ca/EMBOSS/

GDAP - (Found June 19, 2008 )

The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.
http://www.doe-mbi.ucla.edu/Services/GDAP

AnalyCys - (Found June 19, 2008 )

AnalyCys is database for the analysis of conservation and conformation of disulphide bonds in SCOP structural families. This database has a wide range of applications including mapping of disulphide bond mutation patterns, identification of cysteine residues and disulphide bonds important for folding and stabilization, modeling of protein structures and in protein engineering.
http://bioinformatics.univ-reunion.fr/analycys/