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Article ID: 1629 - Last Modified: November 10, 2011

How can I generate dipeptide or tripeptide libraries?

If you have CombiGlide, you can use the Combinatorial Library Enumeration (combgen) program to generate di- or tripeptide libraries. Create an input file (say, dipeptide.in) with the following content:

Core: # No core
Chain: chain-name 2 2
Frag: chain-name 1 peptide
Frag: chain-name 2 peptide

and run the job from the command line with the following command:

$SCHRODINGER/combgen dipeptide

The 'peptide' library includes the 20 standard amino acids plus several alternative ionization and tautomeric states. To use just the 20 standard amino acids, you can create a virtual subset of the 'peptide' library using Vlib commands, as follows:/p>

Core: # No core
Chain: chain-name 2 2
Vlib: new StandardAA peptide all
Vlib: remove StandardAA ARN_(ARG_-H) ASH_(ASP_+H) GLH_(GLU_+H) HIE HIP LYN_(LYS_-H)
Frag: chain-name 1 StandardAA
Frag: chain-name 2 StandardAA

To generate a tripeptide library, change the chain length to 3 and add a fragment library for the third position:

Core: # No core
Chain: chain-name 3 3
Vlib: new StandardAA peptide all
Vlib: remove StandardAA ARN_(ARG_-H) ASH_(ASP_+H) GLH_(GLU_+H) HIE HIP LYN_(LYS_-H)
Frag: chain-name 1 StandardAA
Frag: chain-name 2 StandardAA
Frag: chain-name 3 StandardAA

See Section 11.2 of the CombiGlide User Manual for more information on the combgen program.

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