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External peptide resources

Published on April 7th 2021

We needed a place to find our favourite peptide resources links so we have collected up the following pages in one place as external peptide resources and we hope that people will find it as useful as we do.  Please let us have any suggestions for any other peptide resources that should be here.

ProtParam can 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).

Peptide Mass Calculator - this allows the determination of the mass of any peptide from its sequence.

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.

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.

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

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. 

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. 

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.

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 

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.

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


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