Software

Brief description

M

P

S

3Dee

A database of protein 3D structural domains. No longer maintained but a useful comparison to scop and cath for older structures.

Alscript

Takes multiple protein sequence alignment and produces pretty output for analysis or publication

Amas

Performs sub-family analysis on a multiple protein sequence alignment to identify functionally important residues

Amps

Suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.

Assp

This is software to assess how accurate a secondary structure prediction might be given a particular multiple sequence alignment. It was developed for this paper and may be obtained here.

Domak

Program to identify domains in a protein three-dimensional structure automatically.

GOtcha

Prediction of gene function by application of the Gene Ontology.
22 Oct 2008: Currently unavailable - back soon.

JalView

Multiple sequence alignment workbench. Jalview allows for very flexible editing of alignments, sub-family analysis database lookup and display of features. It exploits SOAP webservices to carry out compute-intensive calculations such as secondary structure prediction and multiple sequence alignment. Jalview also has flexible tools to interrogate and display features obtained from DAS servers.

JNet

Algorithm for protein secondary structure prediction from multiple sequence alingnment. Deployed in JPred server.

JPred

Web server for protein secondary structure prediction, buried site prediction and coiled coils prediction.

Map

Software to search for protein structures similar to a search pattern based on secondary structure and 3D structural constraints.

OBScore

Technique to predict how likely a protein is to succeed in a protein crystallisation pipeline.

OC

General purpose cluster analysis program, only limited by memory and time.

Oxbench

Database of alignments and suite of programs to assess the accuracy of protein multiple sequence alignment methods. This is most useful to developers of such methods!

ParCrys

Software to predict how likely a protein is to succeed in a protein crystallisation pipeline. It uses more features than the OBScore and gives better accuracy.

ProtEST

A server to exploit EST sequence data in protein secondary structure prediction. Now dead.

RHIMS

Server to visualise database search results

Scanps

Software to carry out iterative protein sequence database searching. This is similar to PSI-BLAST, but it uses full dynamic programming and on-the fly statistics to give it the edge over PSI-BLAST when high selectivity is required.

SMERFS

Server to apply a range of conservation calculations to a multiple sequence alignment in order to identify possible functional sites (e.g. protein-protein interface) and display them in Jalview
22 Oct 2008: Currently unavailable - back soon.

SNAPPI

SNAPPI-DB is a database of domain-domain interactions for proteins of known three-dimensional structure. It contains information on the interactions as well as structural multiple alignments of the domains involved all organised according to the SCOP and CATH domain classification hierarchies.

Stamp

Multiple alignment of protein 3D structures. Produces a structure-based sequence alignment with confidence values for each aligned position. Can also be used to search a protein structure database.

TarO

Software system that takes a single protein sequence and runs a large range of analyses on it. These include database searches and structure predictions. The results are tabulated and also presented as an annotated multiple protein sequence alignment.  Although developed to help in selecting proteins for X-ray crystallography, it is of general use for protein analysis.