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Computational chemistry; protein structure; enhanced sampling; molecular dynamics; flexible docking; method development
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Full-Text Articles in Bioinformatics
Development Of An Enhanced Sampling Workflow To Accelerate Molecular Docking With Sparse Biophysical Information, Zachary Stichter
Development Of An Enhanced Sampling Workflow To Accelerate Molecular Docking With Sparse Biophysical Information, Zachary Stichter
Masters Theses & Specialist Projects
Rapid docking of flexible biological macromolecules remains a significant open challenge in protein structure determination. While rigid docking is relatively simple with toolkits such as TagDock, a key obstacle to rapid flexible docking is the complexity and roughness of the free energy surface associated with protein conformational motion (often termed the many-minima problem), meaning conventional molecular dynamics methods do not effectively sample protein conformations near the interaction complex in accessible timescales. Methods such as metadynamics and replica exchange molecular dynamics exist to ameliorate this obstacle, yet these methods use nonphysical biases or random swaps to enhance sampling. In contrast, high …