Linked Life Data

19473861

Source:http://linkedlifedata.com/resource/pubmed/id/19473861

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2009-10-1
pubmed:abstractText
We report the addition of two visualisation algorithms, termed PaperChain and Twister, to the freely available Visual Molecular Dynamics (VMD) package. These algorithms produce visualisations of complex cyclic molecules and multi-branched polysaccharides and are a generalization and optimization of those we previously developed in a standalone package for carbohydrates. PaperChain highlights each ring in a molecular structure with a polygon, which is coloured according to the ring pucker. Twister traces glycosidic bonds with a ribbon that twists according to the relative orientation of successive sugar residues. Combination of these novel algorithms and new ring selection statements with the large set of visualisations already available in VMD allows for unprecedented flexibility in the level of detail displayed for glycoconjugate, glycoprotein and carbohydrate-binding protein structures, as well as other cyclic structures. We highlight the efficacy of these algorithms with selected illustrative examples, clearly demonstrating the value of the new visualisations, not only for structure validation, but also for facilitating insights into molecular structure and mechanism.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-11960986, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-12775711, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-12851408, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-12932195, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-15608187, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-15729334, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-15898788, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-16711210, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-17367125, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-17473875, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-17543889, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-17933765, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-18467126, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-7020376, http://linkedlifedata.com/resource/pubmed/commentcorrection/19473861-9218333
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
1873-4243
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
28
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
131-9
pubmed:dateRevised
2011-9-26
pubmed:meshHeading
pubmed:year
2009
pubmed:articleTitle
Visualisation of cyclic and multi-branched molecules with VMD.
pubmed:affiliation
Computer Science Department, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa. hodgestar@gmail.com
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural