Global Optimization on Funneling Landscapes
Journal of Global Optimization
On the multilevel structure of global optimization problems
Computational Optimization and Applications
Encyclopedia of Optimization
Solving the problem of packing equal and unequal circles in a circular container
Journal of Global Optimization
Guiding the Search for Native-like Protein Conformations with an Ab-initio Tree-based Exploration
International Journal of Robotics Research
Populating Local Minima in the Protein Conformational Space
BIBM '11 Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine
Protein docking with information on evolutionary conserved interfaces
BIBMW '11 Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops
Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy Surface
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
A PCA-guided Search Algorithm to Probe the Conformational Space of the Ras Protein
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Informatics-driven Protein-protein Docking
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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Since its introduction, the basin hopping (BH) framework has proven useful for hard nonlinear optimization problems with multiple variables and modalities. Applications span a wide range, from packing problems in geometry to characterization of molecular states in statistical physics. BH is seeing a reemergence in computational structural biology due to its ability to obtain a coarse-grained representation of the protein energy surface in terms of local minima. In this paper, we show that the BH framework is general and versatile, allowing to address problems related to the characterization of protein structure, assembly, and motion due to its fundamental ability to sample minima in a high-dimensional variable space. We show how specific implementations of the main components in BH yield algorithmic realizations that attain state-of-the-art results in the context of ab initio protein structure prediction and rigid protein-protein docking. We also show that BH can map intermediate minima related with motions connecting diverse stable functionally relevant states in a protein molecule, thus serving as a first step towards the characterization of transition trajectories connecting these states.