uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Fast Flexible Modeling of RNA Structure Using Internal Coordinates
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
Show others and affiliations
2011 (English)In: IEEE/ACM Transactions on Computational Biology & Bioinformatics, ISSN 1545-5963, E-ISSN 1557-9964, Vol. 8, no 5, 1247-1257 p.Article in journal (Refereed) Published
Abstract [en]

Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense.

Place, publisher, year, edition, pages
2011. Vol. 8, no 5, 1247-1257 p.
Keyword [en]
Internal coordinate mechanics, molecular, structure, dynamics, RNA, modeling, prediction, linear, scaling
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:uu:diva-156581DOI: 10.1109/TCBB.2010.104ISI: 000292681800008OAI: oai:DiVA.org:uu-156581DiVA: diva2:432836
Available from: 2011-08-07 Created: 2011-08-04 Last updated: 2011-08-07Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text
By organisation
Computational and Systems Biology
In the same journal
IEEE/ACM Transactions on Computational Biology & Bioinformatics
Biochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 179 hits
ReferencesLink to record
Permanent link

Direct link