Antigenic Peptide Predictions - a great reference on the title subject. The authors have their own online program that predicts the antigenic sequences of proteins.

Helical Wheel - plots a peptide sequence as a helical wheel

Hydrophobicity Plotter - from the Protein Lounge. This online tool allows one to distinguish the hydrophillic and hydrophobic regins of any protein sequence. Choose between Hopps-Woods or Kyte-Doolittle plots.

Isoelectric - plots the charge as a function of pH for any peptide sequence

Isotopident - an online tool that helps you estimate the theoretical isotopic distribution of a peptide from its composition (sequence of amino acids expressed in either 1-letter code, sequence of amino acids expressed in 3-letter code, or its chemical formula). In addition, Isotopident is capable of computing the monoisotopic mass of the peptide sequence. Finally, this tool is also able to predict the most likely isotope combination and the exact mass of peptide.

Moment - makes a contour plot of the helical hydrophobic moment of a peptide sequence.

PAWS - a program provided by Genomic Solutions. PAWS is an acronym which stands for Protein Analysis Work Sheet. The program was originally designed to manipulate protein sequences and perform calculations that aid in the interpretation of mass spectra. It has the capability of mapping mass spectrum information onto sequences as well as saving complex modifications to proteins. PAWS can read a variety of different protein sequence file formats, including most of the common "flat file" formats.

PepSeq - a web based training software package designed for online computer training of peptide sequencing techniques to distance education and on-campus biochemistry students at a university or college.

Peptide Builder Lite - an application that simplifies generation of text representations for simple peptides and proteins. This program features support for both 1 and 3-letter amino-acid notations, on-the-fly calculation of MW, and easy to use interface. One can use your computer keyboard or buttons on the PeptideBuilder screen to enter the amino acid sequences. There are also buttons for placing the complete peptide formula or molecular weight into a clipboard for easy reuse in other Windows applications such as email programs, spreadsheets, etc...

Peptide Companion from CSPS Pharmaceuticals - This software is capable of performing a wide range of peptide analysis: HPLC behavior of peptides, difficult sequences to synthesize, enzymatic or chemical degradation, conformation predictions of peptides and proteins, and much more.

Peptide Cutter - enter a sequence and potential protease cleavage sites and sites cleaved by chemicals in a given protein sequence will be predicted

PeptideMap - creates a peptide map of an amino acid sequence as a function of proteolytic digestion - you choose the enzymes

Peptide Property Calculator #1 - an online tool that calculates molecular weight, plots titration curve and calculates iso-electric point, plots hydrophilicity/hydrophobicity. 1-letter code as well as 3-letter code can be used.

Peptide Property Calculator #2 - from GenScript. Based on the sequence you input, this calculator will determine the chemical formula, isoelectric point, hydrophobicity, and make suggestions on how to solubilize your peptide.

pIcarver - a online tool to visualize theoretical distributions of peptide pI on a given pH range

SIG-Pred: Signal Peptide Prediction