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.

Protein Dipole Server - (Found June 19, 2008 )

The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.
http://bioportal.weizmann.ac.il/dipol/

The Sequence Manipulation Suite 2 - (Found June 19, 2008 )

The Sequence Manipulation Suite is a set of tools for tasks such as sequence format conversion, sequence presentation, analysing sequence characteristics and shuffling or generating random sequences. It can be accessed over the web, or installed locally and run through a web browser.
http://bioinformatics.org/sms2/

The Mendel Site - (Found June 19, 2008 )

The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.
http://mendel.imp.univie.ac.at/mendeljsp/index.jsp

The Amino Acid Repository - (Found June 19, 2008 )

Includes chemical structures and properties, solvent accessibility, post-translational modifications, and more; with references.
http://www.imb-jena.de/IMAGE_AA.html

STING Millenium - (Found June 19, 2008 )

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.
http://trantor.bioc.columbia.edu/SMS/

RPBS - (Found June 19, 2008 )

Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).
http://bioserv.rpbs.jussieu.fr/

RosettaDesign - (Found June 19, 2008 )

RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.
http://rosettadesign.med.unc.edu

Qgrid - (Found June 19, 2008 )

Server which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in proteins.
http://gibk26.bse.kyutech.ac.jp/jouhou/shandar/netasa/qgrid/

ProtParam - (Found June 19, 2008 )

Compute molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.
http://us.expasy.org/tools/protparam.html

PCE - (Found June 19, 2008 )

PCE (Protein Continuum Electrostatics) is an interface to electrostatic potentials and pKa calculations using the MEAD package.
http://bioserv.rpbs.jussieu.fr/Help/PCE.html