Advances and Challenges in Protein-Ligand Docking
Sheng-You Huang,Xiaoqin Zou +1 more
TL;DR: Recent advances of protein flexibility, ligand sampling, and scoring functions—the three important aspects in protein-ligand docking are reviewed.
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Abstract: Molecular docking is a widely-used computational tool for the study of molecular recognition, which aims to predict the binding mode and binding affinity of a complex formed by two or more constituent molecules with known structures. An important type of molecular docking is protein-ligand docking because of its therapeutic applications in modern structure-based drug design. Here, we review the recent advances of protein flexibility, ligand sampling, and scoring functions—the three important aspects in protein-ligand docking. Challenges and possible future directions are discussed in the Conclusion.
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Citations
Molecular Docking and Structure-Based Drug Design Strategies
TL;DR: The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.
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TL;DR: Overall, the ligand binding poses could be identified in most cases by the evaluated docking programs but the ranks of the binding affinities for the entire dataset could not be well predicted by most docking programs.
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A Structure-Based Drug Discovery Paradigm.
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Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview.
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