The program calculates:
Welcome to the Protein Parameters web app for analysing protein sequences. The program performs most of the same functions as the Expasy ProtParam tool, but also allows you to enter a DNA sequence for translation. You can also enter your protein OD280nm once your Protein Parameters have been determined to instantly calculate your protein concentration. Simply select the sequence type (DNA or Protein), enter your sequence and click "Submit".
These sites contain links to many different proteins analysis tools. There is some overlap between them, though they all contain unique links.
Expasy Bioinformatics Resource PortalHuge collection of links to tools provided by the Swiss Institute of Bioinformatics, as well as other sites for everything ranging from protein characterization by ms, pattern and profile searches, post-translational modifications, primary, secondary, tertiary and quaternary structure analysis, molecular modelling and many more!
Health Sciences Library SystemsA truely massive collection of protein analysis tools and databases from the University of Pittsburg.
EMBL-EBIResource for protein search tools (BLAST, FASTA, HMMER, PFAM etc) and many protein-related databases.
NCBI Protein Analysis Tools IndexThis site is presented in the form of a 'workshop' slideshow on Expasy's protein analysis tool. Contains links to many of key resources within Expasy, but with instruction on how to navigate the site and perform comprehensive protein analysis. Great teaching aid.
MolBiol-ToolsHandy smaller portal for a number of protein analysis links, not all of which appear on the Expasy or EMBL sites, including tools for analysing antigenicity, solubility and crystallizability, circular dichroism, mutagenesis etc.
Here are some quick links to some of the most popular sites listed in the portals above.
NCBI BLASTSearch for related protein (or DNA) sequences.
UniProtProtein sequence database
PrositeDatabase of protein domains, families and functional sites
PfamDatabase of protein families represented by multiple sequence alignments and hidden Markov models.
PeptideMassUseful Expasy tool to clave your protein with a selected enzyme and get masses of peptides generated.
ProtScaleAnother Expasy tool that enable you to represent your protein sequence according to various sclaes including hydrophobicity and secondary structure.
RCSB PDBDatabase of protein 3D structures
SwissModelAutomated structure homology server
Click to download results as a pdf file
References
Extinction coefficient
Gill, S.C. and von Hippel, P.H. (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:319-326(1989). PubMed: 2610349
Aliphatic Index
Ikai, A.J. (1980) Thermostability and aliphatic index of globular proteins. J. Biochem. 88, 1895-1898. Pubmed: 7462208
GRAVY
Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132. PubMed: 7108955
pI
Bjellqvist, B., et al. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031. PubMed: 8125050
Bjellqvist, B., et al. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 1994, 15, 529-539. PubMed: 8055880
Wikipedia amino acid pKa values: Wikipedia
The Expasy ProtParam web tool can be found at https://web.expasy.org/protparam/