NDLI: CyloFold: secondary structure prediction including pseudoknots

Content Provider	PubMed Central
Author	Bindewald, Eckart Kluth, Tanner Shapiro, Bruce A.
Copyright Year	2010
Abstract	Computational RNA secondary structure prediction approaches differ by the way RNA pseudoknot interactions are handled. For reasons of computational efficiency, most approaches only allow a limited class of pseudoknot interactions or are not considering them at all. Here we present a computational method for RNA secondary structure prediction that is not restricted in terms of pseudoknot complexity. The approach is based on simulating a folding process in a coarse-grained manner by choosing helices based on established energy rules. The steric feasibility of the chosen set of helices is checked during the folding process using a highly coarse-grained 3D model of the RNA structures. Using two data sets of 26 and 241 RNA sequences we find that this approach is competitive compared to the existing RNA secondary structure prediction programs pknotsRG, HotKnots and UnaFold. The key advantages of the new method are that there is no algorithmic restriction in terms of pseudoknot complexity and a test is made for steric feasibility. Availability: The program is available as web server at the site: http://cylofold.abcc.ncifcrf.gov.
Related Links	http://dx.doi.org/10.1093/nar/gkq432
Starting Page	368
File Format	PDF
ISSN	03051048
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	Web Server issue
Volume Number	38
Language	English
Publisher	Oxford University Press
Publisher Date	2010-07-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

CyloFold: secondary structure prediction including pseudoknots

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

Prediction of RNA secondary structure including pseudoknots for long sequences

HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots

Language models enable zero-shot prediction of RNA secondary structure including pseudoknots

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials

Prediction of consensus RNA secondary structures including pseudoknots

CyloFold: secondary structure prediction including pseudoknots

Similar Documents

CyloFold: secondary structure prediction including pseudoknots

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

Prediction of RNA secondary structure including pseudoknots for long sequences

HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots

Language models enable zero-shot prediction of RNA secondary structure including pseudoknots

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials

Prediction of consensus RNA secondary structures including pseudoknots

CyloFold: secondary structure prediction including pseudoknots