Journal Article10.1007/978-3-031-69162-1_5
Docking and Bias Docking
Juan Manuel Prieto,Gustavo Schottlender,Camila M. Clemente,Rafael Betanzos,Darío Fernández Do Porto,Marcelo A. Martí +5 more
- 01 Jan 2024
- pp 127-148
About: The article was published on 01 Jan 2024. The article focuses on the topics: Docking (animal).
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References
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more
TL;DR: AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in the lab, while also significantly improving the accuracy of the binding mode predictions, judging by tests on the training set used in AutoDock 4 development.
Development and validation of a genetic algorithm for flexible docking.
TL;DR: GOLD (Genetic Optimisation for Ligand Docking) is an automated ligand docking program that uses a genetic algorithm to explore the full range of ligand conformational flexibility with partial flexibility of the protein, and satisfies the fundamental requirement that the ligand must displace loosely bound water on binding.
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Molecular docking: a powerful approach for structure-based drug discovery.
TL;DR: This review presents a brief introduction of the available molecular docking methods, and their development and applications in drug discovery, and a recently developed local move Monte Carlo based approach is introduced.
A Fast Flexible Docking Method using an Incremental Construction Algorithm
TL;DR: This work presents an automatic method for docking organic ligands into protein binding sites that combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand.
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Ligand docking and binding site analysis with PyMOL and Autodock/Vina.
Daniel Seeliger,Bert L. de Groot +1 more
TL;DR: An interface between the popular molecular graphics system PyMOL and the molecular docking suites Autodock and Vina is presented and it is demonstrated how the combination of docking and visualization can aid structure-based drug design efforts.