Using diffusion distances for flexible molecular shape comparison View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-12

AUTHORS

Yu-Shen Liu, Qi Li, Guo-Qin Zheng, Karthik Ramani, William Benjamin

ABSTRACT

BACKGROUND: Many molecules are flexible and undergo significant shape deformation as part of their function, and yet most existing molecular shape comparison (MSC) methods treat them as rigid bodies, which may lead to incorrect shape recognition. RESULTS: In this paper, we present a new shape descriptor, named Diffusion Distance Shape Descriptor (DDSD), for comparing 3D shapes of flexible molecules. The diffusion distance in our work is considered as an average length of paths connecting two landmark points on the molecular shape in a sense of inner distances. The diffusion distance is robust to flexible shape deformation, in particular to topological changes, and it reflects well the molecular structure and deformation without explicit decomposition. Our DDSD is stored as a histogram which is a probability distribution of diffusion distances between all sample point pairs on the molecular surface. Finally, the problem of flexible MSC is reduced to comparison of DDSD histograms. CONCLUSIONS: We illustrate that DDSD is insensitive to shape deformation of flexible molecules and more effective at capturing molecular structures than traditional shape descriptors. The presented algorithm is robust and does not require any prior knowledge of the flexible regions. More... »

PAGES

480

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-11-480

DOI

http://dx.doi.org/10.1186/1471-2105-11-480

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1043040996

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/20868474


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curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-11-480'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-11-480'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-11-480'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-11-480'


 

This table displays all metadata directly associated to this object as RDF triples.

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