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Docking macromolecules with flexible segments
- Source :
- Journal of Computational Chemistry. 24:1910-1920
- Publication Year :
- 2003
- Publisher :
- Wiley, 2003.
-
Abstract
- We address a major obstacle to macromolecular docking algorithms by presenting a new method that takes into account the induced conformational adjustment of flexible loops situated at a protein/macromolecule interface. The method, MC2, is based on a multiple copy representation of the loops, coupled with a Monte Carlo conformational search of the relative position of the macromolecules and their side chain conformations. The selection of optimal loop conformations takes place during Monte Carlo cycling by the iterative adjustment of the weight of each copy. We describe here the parameterization of the method and trials on a protein-DNA complex of known 3-D structure, involving the Drosophila prd paired domain protein and its target oligonucleotide Wenqing, X. et al., Cell1995, 80, 639. We demonstrate that our algorithm can correctly configure and position this protein, despite its relatively complex interactions with both grooves of DNA. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1910–1920, 2003
- Subjects :
- 0303 health sciences
010304 chemical physics
Molecular model
Computer science
Protein domain
Monte Carlo method
General Chemistry
01 natural sciences
03 medical and health sciences
Computational Mathematics
Crystallography
Docking (molecular)
Searching the conformational space for docking
0103 physical sciences
Side chain
Macromolecular docking
Biological system
030304 developmental biology
Macromolecule
Subjects
Details
- ISSN :
- 01928651
- Volume :
- 24
- Database :
- OpenAIRE
- Journal :
- Journal of Computational Chemistry
- Accession number :
- edsair.doi...........9041ca23f5995a49b4c6828911d0b715