Improved packing of protein side chains with parallel ant colonies
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RESEARCH
Open Access
Improved packing of protein side chains with parallel ant colonies Lijun Quan1†, Qiang Lü1,2*†, Haiou Li1, Xiaoyan Xia1,2, Hongjie Wu1,2,3 From IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013) Shanghai, China. 18-21 December 2013
Abstract Introduction: The accurate packing of protein side chains is important for many computational biology problems, such as ab initio protein structure prediction, homology modelling, and protein design and ligand docking applications. Many of existing solutions are modelled as a computational optimisation problem. As well as the design of search algorithms, most solutions suffer from an inaccurate energy function for judging whether a prediction is good or bad. Even if the search has found the lowest energy, there is no certainty of obtaining the protein structures with correct side chains. Methods: We present a side-chain modelling method, pacoPacker, which uses a parallel ant colony optimisation strategy based on sharing a single pheromone matrix. This parallel approach combines different sources of energy functions and generates protein side-chain conformations with the lowest energies jointly determined by the various energy functions. We further optimised the selected rotamers to construct subrotamer by rotamer minimisation, which reasonably improved the discreteness of the rotamer library. Results: We focused on improving the accuracy of side-chain conformation prediction. For a testing set of 442 proteins, 87.19% of X1 and 77.11% of X12 angles were predicted correctly within 40° of the X-ray positions. We compared the accuracy of pacoPacker with state-of-the-art methods, such as CIS-RR and SCWRL4. We analysed the results from different perspectives, in terms of protein chain and individual residues. In this comprehensive benchmark testing, 51.5% of proteins within a length of 400 amino acids predicted by pacoPacker were superior to the results of CIS-RR and SCWRL4 simultaneously. Finally, we also showed the advantage of using the subrotamers strategy. All results confirmed that our parallel approach is competitive to state-of-the-art solutions for packing side chains. Conclusions: This parallel approach combines various sources of searching intelligence and energy functions to pack protein side chains. It provides a frame-work for combining different inaccuracy/usefulness objective functions by designing parallel heuristic search algorithms.
Introduction The accurate packing of side chains plays a very important role in modelling protein structures. In ab initio structure prediction, the goal is to choose a rotamer for each position so that the molecule is close to the natural structure. In homology modelling, the goal is to predict the structure of a protein that is homologous to another of a known * Correspondence: [email protected] † Contributed equally 1 School of Computer Science and Technology, Soochow University, Suzhou, 215006, China Full list of author information is available at the end of the article
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