External peptide resources

The links on this page are to external peptide resources useful for calculating the properties of peptides

ProtParam

Use ProtParam to determine physical and chemical parameters for a given protein in Swiss-Prot or TrEMBL or for a user entered sequence. Parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY)

https://web.expasy.org/protparam/

Peptide Mass Calculator

The peptide mass calculator allows the determination of the mass of any peptide from its sequence:

http://rna.rega.kuleuven.be/masspec/pepcalc.htm

Pepwheel

Pepwheel draws a helical wheel diagram for a protein sequence. Pepwheel displays the sequence in a helical representation as if looking down the axis of the helix. Pepwheel is useful for highlighting the amphipathicity of a peptide

http://www.bioinformatics.nl/cgi-bin/emboss/pepwheel

Pepdraw

Pepdraw allows the calculation of various properties of a peptide from its sequence including length, mass, isoelectric point, net charge, hydrophobicity and extinction coefficients:

http://www.tulane.edu/~biochem/WW/PepDraw/

Shuffle Protein

Shuffle Protein randomly shuffles a protein sequence. Shuffled sequences can be used to evaluate the significance of sequence analysis results

http://www.bioinformatics.org/sms2/shuffle_protein.html

ProtScale

ProtScale allows analysis of the profile produced by an amino acid scale on a selected protein. An amino acid scale is a numerical value assigned to each type of amino acid, and protscale allows analysis on 57 predefined scales entered from the literature, including molecular weight, number of codons, bulkiness, polarity, refractivity, conformation and more.

https://web.expasy.org/protscale/

PeptideMass

PeptideMass cleaves a protein sequence from the UniProt Knowledgebase (Swiss-Prot and TrEMBL), or a user-entered protein sequence with a chosen enzyme, and calculates the masses of the generated peptides and can also calculate theoretical isoelectric point and mass values. Additionally PeptideMass can return the mass of peptides known to carry post-translational modifications, and highlight peptides whose masses may be affected by database conflicts, polymorphisms or splice variants

https://web.expasy.org/peptide_mass/

Blast

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. Blast compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blastho me

Mass, Elemental Composition, Amino Acid Composition, Isotope Ratio Data

Use this tool to calculate the mass, elemental and amino acid composition, and ratio of M+1 and M+2 peaks relative to the M peak of a peptide

https://www.pep-calc.com/

Protein Stats

Protein Stats allows the determination of the number of occurrences of each residue in a sequence. Percentage totals are also given for each residue, and certain groups of residues, allowing comparison of results for different sequences

http://www.bioinformatics.org/sms2/protein_stats.html

Convert three letter amino acid codes to single letters and vice versa

Use this tool to interconvert three and one letter amino acid codes

https://www.bioinformatics.org/sms2/one_to_three.html