Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1414)

Abstract

We introduce two GALAXY web servers called GalaxySite and GalaxyPepDock that predict protein complex structures with small organic compounds and peptides, respectively. GalaxySite predicts ligands that may bind the input protein and generates complex structures of the protein with the predicted ligands from the protein structure given as input or predicted from the input sequence. GalaxyPepDock takes a protein structure and a peptide sequence as input and predicts structures for the protein–peptide complex. Both GalaxySite and GalaxyPepDock rely on available experimentally resolved structures of protein–ligand complexes evolutionarily related to the target. With the continuously increasing size of the protein structure database, the probability of finding related proteins in the database is increasing. The servers further relax the complex structures to refine the structural aspects that are missing in the available structures or that are not compatible with the given protein by optimizing physicochemical interactions. GalaxyPepDock allows conformational change of the protein receptor induced by peptide binding. The atomistic interactions with ligands predicted by the GALAXY servers may offer important clues for designing new molecules or proteins with desired binding properties.

Key words

GALAXY Binding site prediction Peptide docking Ligand docking Ligand design 

Notes

Acknowledgement

This work was supported by the National Research Foundation of Korea grants funded by the Ministry of Science, ICT & Future Planning (No. 2013R1A2A1A09012229).

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of ChemistrySeoul National UniversitySeoulRepublic of Korea

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