Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 11, Issue 8, Pages 3016-3034Publisher
MDPI
DOI: 10.3390/ijms11083016
Keywords
protein flexibility; ligand sampling; scoring functions; molecular docking; protein-ligand interactions
Funding
- NIH [R21GM088517]
- Cystic Fibrosis Foundation [ZOU07I0]
- Research Board Award [RB-07-32]
- University of Missouri [URC 09-004]
- Dell
- SGI
- Sun Microsystems
- TimeLogic
- Intel
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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 import ant 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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