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Macromolecular docking

Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Protein–protein complexes are the most commonly attempted targets of such modelling, followed by protein–nucleic acid complexes.

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Rigid-body docking vs. flexible docking

Methods

Evaluation

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Macromolecular docking

Nodes75
Edges74
Triples3
Avg. degree1.97
Density0.026667
Components1

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Macromolecular docking

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Macromolecular docking → computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules

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Important terminology

docking protein complexes scoring benchmark functions proteins structure may complex modelling structures biological also methods cases interactions used binding configurations

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SubjectPredicateObjectConfidenceSrc
Macromolecular dockingis acomputational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules0.90text
scoring functions to identify structures that are most likely to occur in nature.The terminstance ofThese candidates must be ranked using methods0.80text
CHARMM or AMBER.Phylogenetic desirability of the interacting regions.Clustering coefficients.Information based cues.It is usual to create hybrid scores by combining one or more categories above in a weighted sum whose weights are optimized on cases from the benchmarkinstance ofestimated using parameters from molecular mechanics force fields0.80text

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