Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains
Joint Authors
Smith, Cameron
Backofen, Rolf
Deane, Charlotte M.
Saunders, Rhodri
Mann, Martin
Source
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-6, 6 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-08-15
Country of Publication
Egypt
No. of Pages
6
Main Subjects
Natural & Life Sciences (Multidisciplinary)
Biology
Abstract EN
Lattice models are a common abstraction used in the study of protein structure, folding, and refinement.
They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible.
Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently.
We introduce LatFit, a new tool to produce high-accuracy lattice protein models.
It generates both backbone-only and backbone-side-chain models in any user defined lattice.
LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method.
We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk.
Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice).
To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models.
American Psychological Association (APA)
Mann, Martin& Saunders, Rhodri& Smith, Cameron& Backofen, Rolf& Deane, Charlotte M.. 2012. Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains. Advances in Bioinformatics،Vol. 2012, no. 2012, pp.1-6.
https://search.emarefa.net/detail/BIM-449565
Modern Language Association (MLA)
Mann, Martin…[et al.]. Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains. Advances in Bioinformatics No. 2012 (2012), pp.1-6.
https://search.emarefa.net/detail/BIM-449565
American Medical Association (AMA)
Mann, Martin& Saunders, Rhodri& Smith, Cameron& Backofen, Rolf& Deane, Charlotte M.. Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains. Advances in Bioinformatics. 2012. Vol. 2012, no. 2012, pp.1-6.
https://search.emarefa.net/detail/BIM-449565
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-449565