Protein flexibility in ligand docking and virtual screening to protein kinases.
By Claudio N. Cavasotto, Ruben Abagyan. Journal of Molecular Biology, 2004
393 citations recorded by the source corpus.
Subfields: Computational Theory and Mathematics, Molecular Biology, Organic Chemistry
View Paper: https://www.semanticscholar.org/paper/2ee021fbea91a72505f0d90023f95245e2b24a93
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Computational Theory and Mathematics
- Shengyou Huang
- John Karanicolas
- Xiaoqin Zou
- David K. Johnson
- Hong-Xing Zhang
- Sandeepkumar Kothiwale
- Jens Meiler
- E. W. Lowe
In Molecular Biology
- Shengyou Huang
- John Karanicolas
- Xiaoqin Zou
- David K. Johnson
- Hong-Xing Zhang
- Sandeepkumar Kothiwale
- Jens Meiler
- E. W. Lowe
In Organic Chemistry
- Shengyou Huang
- John Karanicolas
- David K. Johnson
- Xiaoqin Zou
- Hong-Xing Zhang
- Sandeepkumar Kothiwale
- Jens Meiler
- E. W. Lowe
Citations in the corpus
- Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking (2006, methodology): “31 Therefore, we further evaluated the performance of scoring predictions with different docking methods, which is especially important for virtual database screening.”
- Computational Methods in Drug Discovery (2014, background): “Mimicking conformational change of kinases, and not just side-chain flexibility, improves the success of kinase inhibitor docking (Cavasotto and Abagyan, 2004; Rabiller et al., 2010).”
- Protein-protein docking with backbone flexibility. (2007, neutral): “21,22 ICM has been used for protein– protein docking with side-chain flexibility(23) and protein–ligand docking with backbone flexibility.(24) “Treelike” topologies have also been implemented in X-ray and NMR refinement packages such as CNS(25) and XPLOR-NIH,(26) which perform molecular dynamics in ”
- Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations (2015, positive): “Ensemble docking Already others have noted that docking against multiple receptor conformations (“ensemble docking”) can enhance performance relative to docking against a single static conformation (152-160).”
- Molecular docking: a powerful approach for structure-based drug discovery. (2011, methodology): “IFREDA [115] utilizes a hybrid method that combines soft potential and multiple receptor conformations, accounting for receptor flexibility.”
- ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility (2006, neutral): “22 The success rate is (cid:2) 65% when using the 2 A˚ RMSD criteria for ligand atoms only.”
- Advances and Challenges in Protein-Ligand Docking (2010, methodology): “simulations, Monte Carlo simulations, or structure prediction have also been used to account for protein flexibility [35–43].”