Milton Saier's molecular analysis tools for peptide sequences.
UCSD Transport System Databases, Phylogenetic analysis and related molecular analysis tools.
Hydrophobicity, other conformational parameters, etc.
Predict the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive and Gram-negative prokaryotes, and eukaryotes. Includes a PSort help manual.
This Java applet translates proteins into nucleotide sequences with adapted codon usage. This allows optimisation of a sequence for expression in specific organisms. From Entelechon.com.
TMpred program makes a prediction of membrane-spanning regions and their orientation.
An Automated Comparative Protein Modeling Server at ExPASy
Brookhaven Structure Database
Simple Keyword search of the Brookhaven Structure Database. Retrieve X-ray crystallography cooordinates for display by RasMol. Rasmol for a variety of platforms can be obtained from ftp.dcs.ed.ac.uk/pub/rasmol/
This program, analyses proteins for statistically significant features like charge-clusters, repeats, hydrophobic regions, compositional domains etc. One of its options is to generate self-explanatory output