PROTEIN CHEMISTRY BACKGROUND INFORMATION: You might want to consult Robert Russell's Guide to Structure Prediction.   For the biochemical properties of amino acids see PROWL, Amino Acid Hydrophobicity and Aminosauren. If you  are specifically interested in antibodies I would recommend that you visit "The Antibody Resource Page."

Table of amino acid abbreviations

Amino acid composition, mass & pI:

 Amino acid composition & Mass – ProtParam tool (ExPASy, Switzerland)
Isoelectric Point - Compute pI/Mw tool (ExPASy, Switzerland). If you want a plot of the relationship between charge and pH use ProteinChemist (ProteinChemist.com) or JVirGel Proteomic Tools (PRODORIC Net, Germany).  
Mass, pI, composition and mol% acidic, basic, aromatic, polar etc. amino acids - PEPSTATS (Institut Pasteur, France). Biochemistry-online (Vitalonic, Russia) gives one % composition, molecular weight, pI, and charge at any desired pH.

Protein calculator (C. Putnam, The Scripps Research Institute, U.S.A.) - calculates mass, pI, charge at a given pH, counts amino acid residues etc.

Antigenicity and Allergenicity:

  Abie Pro Peptide Antibody Design (Chang Bioscience)

  EVALLER - allows for bioinformatics assessment of proteins in the context of allergenicity (type-I hypersensitivity).

 SBS EpiToolKit  -  provides a collection of methods from computational immunology for the prediction of MHC ligands or potential T-Cell epitopes. Additionally, SNEPv2 extends epitope prediction by the possibility to analyze the influence of protein polymorphisms on the immunogenicity of the arising polymorphic peptides. (Reference: N.C. Toussaint & O. Kohlbacher. 2009. Nucl. Acids Res. 37 (Web server issue): W617-W622 )

Antimicrobial peptides:

 AMPer: A Database and an Automated Discovery Tool for Antimicrobial Peptides. (Reference: C.J. D. Fjell et al. 2007. Bioinformatics)

Circular Dichroism:

Circular Dichroism (Birkbeck College, School of Crystalography, England) "DICHROWEB is an interactive web site which allows the deconvolution of data from Circular Dichroism spectroscopy experiments. It offers an interface to a range of deconvolution algorithms (CONTINLL, SELCON3, CDSSTR, VARSLC, K2D)."
K2d: Prediction of percentages of protein secondary structure from CD spectra - allows analysis of 41 CD spectrum data points ranging from 200 nm to 240 nm (Dr. Miguel A. Andrade, EMBL)

Cysteine Residues:

DiANNA - will predict cysteine oxidation state (76% accuracy),  cysteine pairs (81% accuracy) and disulfide bond connectivity (86% accuracy). (Reference: F. Ferrè & P. Clote. 2005. Nucl. Acids Res.  33: W230-W232).

CYSREDOX (Rockefeller University, U.S.A.) and CYSPRED (CIRB Biocomputing Group, University of Bologna, Italy) calculate the redox state of cysteine residues in proteins.

Prediction of Cys-Cys linkages in proteins - achieves a prediction accuracy of 63% (Reference: C-H. Tsai et al. 2005. Bioinformatics 21: 4416-4419.)

Hydrophobicity Plotter (Viral Bioinformatics Resource Center, University of Victoria, Canada) - this Java applet graphs the hydrophobicity/ hydrophilicity of a sequence of amino acids, using a sliding window. The window size can be specified by the user, and several hydrophobicity scales (Kyte-Doolittle, Hopp-Woods or Parker-Guo-Hodgescan) can be chosen. 

Proteolysis and Mass Spectrometry:

Proteolysis -  PeptideCutter (ExPASy, Switzerland) which also predicts cleavage sites for enzymes and chemicals. An alternative proteolysis site is Mobility_plot 4.1 (Advanced Proteolytic Fingerprinting, IGH, France).  
For more sophisticated protein analysis involving mass spectroscopy ExPasy has introduced FindMod tool to predict potential protein post-translational modifications in peptides; and, GlycoMod Tool which can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses.

ProFound - is a tool for searching a protein sequence database using information from mass spectra of peptide maps. A Bayesian algorithm is used to rank the protein sequences in the database according to their probability of producing the peptide map. A simplified version can be accessed here (Rockefeller University, New York, U.S.A.)  or here. In neither case can one use one's own protein database.

PepFrag (Rockefeller University, New York, U.S.A.) - is a tool for searching protein or nucleotide sequences using information from fragmentation mass spectra of peptides.

  ProteinProspector (University of California) -  offers a wide variety of tools (e.g. MS-Fit, MS-Tag, MS-Seq, MS-Pattern, MS-Homology) for the protein mass spectroscopist.

Repeats:

Repeats in protein sequences can be discovered using Radar (Rapid Automatic Detection and Alignment of Repeats, European Bioinformatics Institute) or Rep (European Molecular Biology Laboratory, Germany). The former is a general search engine while the latter screens for specific repeat families.  Another useful site is Internal Repeat Finder (UCLA-DOE Institute for Genomics & Proteomics, U.S.A.).

REPPER (REPeats and their PERiodicities) - detects and analyzes regions with short gapless repeats in proteins. It finds periodicities by Fourier Transform (FTwin) and internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids that reflect certain properties, for instance hydrophobicity, and gives information on corresponding periodicities. REPwin uses self-alignments and displays repeats that reveal significant internal similarities. They are complemented by PSIPRED and coiled coil prediction (COILS), making the server a useful analytical tool for fibrous proteins. (Reference: M. Gruber et al. 2005. Nucl. Acids Res. 33: W239-W243).

Two-dimensional gels:

JVirGel calculation of virtual two-dimensional protein gels.   - creates virtual 2D proteomes from a huge list of eukaryotes & prokaryotes (or an individual protein). Two versions: html (limited) and Java applet (incredible but you need to install Java Runtime Environment. (Reference: K. Hiller et al. 2003. Nucl. Acids Res. 31: 3862-3865).

Gelprint (Information Genomique et Structurale, France) - generates an in silico 2D-gel from the theoretical pI (isoelectric point) and Mw (molecular weight) data for a set of proteins. Comparisons of the in silico 2D-gel with your real 2D-gel generated by two-dimensional poyacrylamide gel electrophoresis (2D-PAGE) may help you to identify proteins of your interest. In addition, the in silico data is scaled to fit to your real gel.

Draw Virtual Two-Dimensional Protein Gels (PRODORIC Net, Germany) - using your own protein sequence data or for different organisms. 

FLICKER - (Laboratory of Experimental and Computational Biology, Germany). Flicker is a method for comparing images, such as two 2-D gels from different Internet sources on your Web browser. Choose "compare".

I-Mutant2.0: predictor of protein stability changes upon mutation  - choose either a PDB reference number or paste your own protein. The answer (by email) indicates whether he protein is more or less stable, a fact which could be of use in designing "better" proteins.  (Reference: E. Capriotti et al. 2005. Nucl. Acids Res. 33: W306-W310).

Metasite:

 Scratch Protein Predictor - (Institute for Genomics and Bioinformatics, University California, Irvine) - programs include: ACCpro: the relative solvent accessibility of protein residues; CMAPpro: Prediction of amino acid contact maps; COBEpro: Prediction of continuous B-cell epitopes; CONpro: predicts whether the number of contacts of each residue in a protein is above or below the average for that residue; DIpro: Prediction of disulphide bridges; DISpro: Prediction of disordered regions; DOMpro: Prediction of domains; SSpro: Prediction of protein secondary structure; SVMcon: Prediction of amino acid contact maps using Support Vector Machines; and, 3Dpro: Prediction of protein tertiary structure (Ab Initio).