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Open Access Research

MORPH-PRO: a novel algorithm and web server for protein morphing

Natalie E Castellana1, Andrey Lushnikov4, Piotr Rotkiewicz2, Natasha Sefcovic3, Pavel A Pevzner14, Adam Godzik2 and Kira Vyatkina4*

Author Affiliations

1 Department of Computer Science, University of California-San Diego, La Jolla, CA USA

2 Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA USA

3 Joint Center for Structural Genomics, Bioinformatics Core, University of California-San Diego, La Jolla, CA USA

4 Algorithmic Biology Laboratory, Saint Petersburg Academic University, Saint Petersburg, Russia

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Algorithms for Molecular Biology 2013, 8:19  doi:10.1186/1748-7188-8-19

Published: 11 July 2013

Abstract

Background

Proteins are known to be dynamic in nature, changing from one conformation to another while performing vital cellular tasks. It is important to understand these movements in order to better understand protein function. At the same time, experimental techniques provide us with only single snapshots of the whole ensemble of available conformations. Computational protein morphing provides a visualization of a protein structure transitioning from one conformation to another by producing a series of intermediate conformations.

Results

We present a novel, efficient morphing algorithm, MORPH-PRO based on linear interpolation. We also show that apart from visualization, morphing can be used to provide plausible intermediate structures. We test this by using the intermediate structures of a c-Jun N-terminal kinase (JNK1) conformational change in a virtual docking experiment. The structures are shown to dock with higher score to known JNK1-binding ligands than structures solved using X-Ray crystallography. This experiment demonstrates the potential applications of the intermediate structures in modeling or virtual screening efforts.

Conclusions

Visualization of protein conformational changes is important for characterization of protein function. Furthermore, the intermediate structures produced by our algorithm are good approximations to true structures. We believe there is great potential for these computationally predicted structures in protein-ligand docking experiments and virtual screening. The MORPH-PRO web server can be accessed at http://morph-pro.bioinf.spbau.ru webcite.

Keywords:
Protein morphing; Molecular docking; Virtual screening