• Peptide Calculator:
  • Sequences can be entered in upper case, lower case or mixed case.
  • Select an N-terminal for your peptide.  If you select nothing the default is a free amine.
  • Select a linker.  This is optional.  If you select nothing the default is no linker.
  • Enter your peptide sequence in the text area by using the keyboard or pasting your sequence.
  • Enter 'J' for phoshhoSerine, 'U' for phosphoThreonine and 'O' for phosphoTyrosine and 'Z 'for Norleucine.
  • Enter 'X' for (S)-2(4'-pentenyl)Alanine.  Your sequence must contain two X's.
  • Select a C-terminal for your peptide.  If you select nothing the default is carboxylic acid.
  • The default molecular weight is average.  Use the option button for monoisotopic weights.
  • The default molecular weight is for linear peptides. 
  • Use the 'disulfide-bridged' option buttons for disulfide-bridged peptides. One can select upto three disulfide bridges.
  • Use the 'lactam' option buttons for lactam bridged peptides.  Lactam bridged peptides must contain at least one 'D' (or 'E') and one 'K' in the sequence.
  • Use the 'cyclic' option button for head to tail cyclic peptides.  Cyclic peptides must have 'acid' as the C-terminus and 'amine' as the N-terminus.
  • Use the 'stapled' option button for hydrocarbon stapled peptides.  Your sequence should contain only two X's [(S)-2(4-pentenyl)Alanine] for hydrocarbon stapled peptides.

  • Analog Calculator:
  • The analog calculator can be used to calculate the molecular weights of standard peptides, disulfide-bridged peptides, lactam-bridged peptides, cyclic peptides, hydrocarbon stapled peptides, peptides containing analogs, pyrrole-imidazole polyamides, peptide-pyrrole-imidazole conjugates and peptide-pna conjugates.
  • Amino acids or analogs have to selected from the dropdown buttons. Click "add amino acid" button after each amino acid is selected. Click "calculate" to calculate the molecular weight of the peptide. Molecular weigts are monoisotopic in the analog calculator.
  • Click the disulfide bridge option buttons for disulfide bridges. Peptides must contain at least two cysteines to have a disulfide bridge.
  • Alkeneyl residues are listed as modfications of Alanine under the 'A' dropdown button. Use these for hydrocarbon stapled peptides. Peptides must have two alkenyl groups to be hydrocarbon stapled.
  • C-terminal linkers like C-terminal DimainePEG and C-terminal EtyhlDiamine are listed as analogs of 'X'. Other likers like Abu, AHx, PEG2, PEG3 etc are also listed as analogs of 'X'.
  • PNA bases and the PNA AEEA spacer are listed as analogs of 'X'. The analog calculator can be used to calculate the molecular weights of either stand alone PNA or peptide-PNA conjugates using appropriate linkers.
  • Pyrrole monomers, imidazole monomers, GABA, beta alanine etc. are listed as analogs of 'X'. The analog calculator can be used to calculate the molecular weights of either Py-Im polyamides or peptide-Py-Im conjugates using appropriate linkers.

  • PNA Calculator:
  • The stand alone PNA calculator can be used to calculate the molecular weights of peptide nucleic acids (PNA).
  • PNA sequences can be entered in upper case, lower case or a mixture of cases.  Sequences can also be pasted.  The PNA calculator will convert all characters to lower case.
  • Valid PNA characters are 'a', 't', 'g' and 'c'.  Any other character will give an error.
  • The default N-terminus for PNA is free amine.  Select the 'O' linker for the commonly used PNA AEEA spacer.
  • The default C-terminus for PNA is amide.  Select 'Lysine' or 'Lysine-Amide' if you need these instead.

  • Polyamide Calculator:
  • The stand alone Polyamide calculator can be used to calculate the molecular weights of pyrrole imidazole polyamides.
  • Use the buttons to select pyrrole, imidazole, gama aminobutyric acid or betaalanine.
  • The default N-terminus for polyamides is free amine. Use the N-terminus dropdown for another selection.
  • The default C-terminus for polyamides is acid. Use the C-terminus dropdown to select amide, Dp or BDp.

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