GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization

By Hasup Lee, Lim Heo, Myeong Sup Lee, Chaok Seok. 2015

273 citations recorded by the source corpus.

Protein–peptide interactions are involved in a wide range of biological processes and are attractive targets for therapeutic purposes because of their small interfaces. Therefore, effective protein–peptide docking techniques can provide the basis for potential therapeutic applications by enabling an atomic-level understanding of protein interactions. With the increasing number of protein–peptide structures deposited in the protein data bank, the prediction accuracy of protein-peptide docking can be enhanced by utilizing the information provided by the database. The GalaxyPepDock web server, which is freely accessible at http://galaxy.seoklab.org/pepdock, performs similarity-based docking by finding templates from the database of experimentally determined structures and building models using energy-based optimization that allows for structural flexibility. The server can therefore effectively model the structural differences between the template and target protein–peptide complexes. The performance of GalaxyPepDock is superior to those of the other currently available web servers when tested on the PeptiDB set and on recently released complex structures. When tested on the CAPRI target 67, GalaxyPepDock generates models that are more accurate than the best server models submitted during the CAPRI blind prediction experiment.

Subfields: Computational Theory and Mathematics, Oncology, Organic Chemistry

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Pei-Zhang Zhou
2. Bowen Jin
3. Shengyou Huang
4. Pierre Tufféry
5. Xiaoqin Zou
6. Yumeng Yan

In Oncology

1. Bowen Jin
2. Shengyou Huang
3. Pei-Zhang Zhou

In Organic Chemistry

1. Bowen Jin
2. Pei-Zhang Zhou
3. Shengyou Huang
4. Xiaoqin Zou

Citations in the corpus

• A Comprehensive Review on Current Advances in Peptide Drug Development and Design (2019, methodology): “The GalaxyPepDock is a popular server that performs such similarity-based docking by searching templates of highest similarity and builds models using energy optimization to allow more accurate predictions on structural flexibility between interacting complexes [110].”
• HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm (2018, background): “To address these challenges, a variety of state-of-the-art algorithms have been developed for protein–peptide docking in the past few years (5–16).”
• PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex (2016, methodology): “The RosettaFlexPepDock (19) server will refine the structure of a peptide bound to a receptor, Galaxypepdock (20) performs similarity based docking using existing templates and the CABS-dock server (21) performs a blind docking which can be time consuming.”