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Thomas C. Bishop

dblp:27/7593 · DBLP profile ↗
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1ranked-venue papers
1as first author
0since 2021 · last 2009
—ORCID · unresolved

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › structural bioinformatics › nucleic acid structure analysis
DNA structure modeling
0.112009
VDNA: The virtual DNA plug-in for VMD · Bioinform. 2009
Bioinformatics and computational biology › molecular informatics › molecular modeling
molecular structure modeling
0.112009
VDNA: The virtual DNA plug-in for VMD · Bioinform. 2009
Bioinformatics and computational biology › molecular informatics
molecular visualization
0.012009
VDNA: The virtual DNA plug-in for VMD · Bioinform. 2009

Methods — techniques the papers use, named apart from their topics

mathematical expression-based modeling · 0.1coarse-grained modeling · 0.1
YearPublicationVenuePosition
2009 VDNA: The virtual DNA plug-in for VMD
abstract
UNLABELLED: The DNA inter base pair step parameters (Tilt, Roll, Twist, Shift, Slide, Rise) are a standard internal coordinate representation of DNA. In the absence of bend and shear, it is relatively easy to mentally visualize how Twist and Rise generate the familiar double helix. More complex structures do not readily yield to such intuition. For this reason, we developed a plug-in for VMD that accepts a set of mathematical expressions as input and generates a coarse-grained model of DNA as output. This feature of VDNA appears to provide a unique approach to DNA modeling. Predefined expressions include: linear, sheared, bent and circular DNA, and models of the nucleosome superhelix, chromatin, thermal motion and nucleosome unwrapping. AVAILABILITY: VDNA is pre-installed in VMD, http://www.ks.uiuc.edu/Research/vmd. Updates are at http://dna.ccs.tulane.edu.
Thomas C. Bishop
Bioinform.1