Linked Life Data

11472090

Source:http://linkedlifedata.com/resource/pubmed/id/11472090

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2-3
pubmed:dateCreated
2001-7-26
pubmed:abstractText
We describe here a set of multiresolution visualization and docking procedures that we refer to as the Situs package. The package was developed to provide an efficient and robust method for the fitting of atomic structures into low-resolution data. The current release was optimized specifically for the visualization and docking of single molecules. A novel 3D graphics viewer, volslice3d, was developed for the package to provide an immersive virtual reality environment for measuring and rendering volumetric data sets. The precision of single-molecule, rigid-body docking was tested on simulated (noise-free) low-resolution density maps. For spatial resolutions near 20 A typically arising in electron microscopy image reconstructions, a docking precision on the order of 1 A can be achieved. The shape-matching score captured the correct solutions in all 10 trial cases and was sufficiently stringent to yield unique matches in 8 systems. Novel routines were developed for the flexible docking of atomic structures whose shape deviates from the corresponding low-resolution shape. Test calculations on isoforms of actin and lactoferrin demonstrate that the flexible docking faithfully reproduces conformational differences with a precision < 2 A if atomic structures are locally conserved.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:issn
1047-8477
pubmed:author
pubmed:copyrightInfo
Copyright 2001 Academic Press.
pubmed:issnType
Print
pubmed:volume
133
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
193-202
pubmed:dateRevised
2011-11-17
pubmed:meshHeading
pubmed:articleTitle
Using situs for flexible and rigid-body fitting of multiresolution single-molecule data.
pubmed:affiliation
Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA. wriggers@scripps.edu
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S.