In this article, Senior Application Scientist Thijs Beuming discusses the development of a new Glide docking protocol designed specifically for peptides.
CycloPs is a software for generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids.
Here is the abstract from Pubmed:
We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dimensional SMILES and three-dimensional SDF formats, suitable for virtual screening. The stand-alone software is capable of filtering the virtual libraries using empirical measurements, including peptide synthesizability by standard peptide synthesis techniques, stability, and the druglike properties of the peptide. The software and accompanying Web interface is designed to enable the rapid generation of large, structurally diverse, synthesizable virtual libraries of constrained peptides quickly and conveniently, for use in virtual screening experiments. The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptide, are available at http://bioware.ucd.ie .
Some programs that I have found to perform peptide docking:
1) Rosetta FlexPepDock is a high-resolution peptide docking (refinement) protocol, implemented within the Rosetta framework. The input for this server is a PDB file of a complex between a protein receptor (first chain) and an estimated conformation for a peptide (second chain). FlexPepDock was shown to be able to accurately refine the peptide structure starting from up to 5.5A RMSD of the native conformation, allowing full flexibility to the peptide and side-chain flexibility to the receptor.
2) Autodock. Autodock itselft as well as PSO@Autodock can be used to dock small peptides on a protein.
3) eHiTS. See also
4) ICM-Dock. Flexible peptide-receptor docking.
A useful link listing many of the docking programs and their capabilities can be found here.
If you happen to know of more programs please let us know!
Alexis, Isidora, Michalis, Danai, Panos, Celia, Klea, Zoe
lab group members!
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