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.

Onto-Tools - (Found June 19, 2008 )

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.
http://vortex.cs.wayne.edu/Projects.html

H++ - (Found June 19, 2008 )

H++ is a tool for the prediction of protonation states and pK of ionizable groups in macromolecular structures.
http://biophysics.cs.vt.edu/H++

IBM Bioinformatics and Pattern Discovery Group - (Found June 19, 2008 )

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.
http://cbcsrv.watson.ibm.com/Tspd.html

JPD - (Found June 19, 2008 )

Java Protein Dossier (JPD) is part of the STING Suite of web based programs for visualization and analyses of molecular structures. JPD can display many different physicochemical parameters for PDB files as well as for structurally aligned pairs of PDB files.
http://trantor.bioc.columbia.edu/SMS/JPD/

LINKER - (Found June 19, 2008 )

LINKER is a tool for designing linker peptide sequences for use in the construction of fusion proteins. The user provides the desired length of the linker in either Angstroms or number of residues, and several other constraints may also be specified, including the inclusion or exclusion of certain amino acids or protease sensitive sites.
http://astro.temple.edu/~feng/Servers/BioinformaticServers.htm

MASCOT (Matrix Science) - (Found June 19, 2008 )

Protein identification by peptide mass; excellent documentation; incorporates code from MOWSE but allows more search methods on more sequence databases.
http://www.matrixscience.com/

MODi - (Found June 19, 2008 )

Modi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.
http://modi.uos.ac.kr/modi/

MolSurfer - (Found June 19, 2008 )

Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNARNA interfaces.
http://projects.villa-bosch.de/dbase/molsurfer/

MONSTER - (Found June 19, 2008 )

MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.
http://monster.northwestern.edu/

MPI Toolkit - (Found June 19, 2008 )

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.
http://toolkit.tuebingen.mpg.de