Abstract
Molecular docking is a typical method of structure-based drug design. It aims to identify a ligand that binds to a specific receptor binding site and determine its most favorable binding pose. A new multi-objective optimization method is introduced to improve the docking accuracy. Two diverse scoring functions, energy-based and contact-based, are applied to demonstrate the multi-objective strategy. The energy-based scoring function is a force field one which consists of the Coulomb and Van der Waals terms. The contact-based one is a simple summation of the number of heavy atom contacts between ligand and receptor. The flexibility of receptor is considered by modeling the residue groups movements that occur during the interaction. A new multi-objective docking program that accounts for protein flexibility has been developed. An adaptive multi-generation evolutionary algorithm is adopted to solve the optimization problem. Results show that the method can give more robust and reasonable conformation of ligand in molecular docking.
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Acknowledgement
The author gratefully acknowledges financial support for this work from the Foundation of Liaoning Education Ministry (No. L2015037).
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Kang, L. (2019). Refined Molecular Docking with Multi-objective Optimization Method. In: Xiong, N., Xiao, Z., Tong, Z., Du, J., Wang, L., Li, M. (eds) Advances in Computational Science and Computing. ISCSC 2018 2018. Advances in Intelligent Systems and Computing, vol 877. Springer, Cham. https://doi.org/10.1007/978-3-030-02116-0_7
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