Structure clustering features on the Sfold Web server

Bioinformatics

Volumn 21, Issue 20, 2005, Pages 3926-3928

  Chan, Chi Yu ^a   Lawrence, Charles E ^a,b   Ding, Ye ^a  

^a NEW YORK STATE DEPARTMENT OF HEALTH   (United States)

^b BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEASE P; RNA;

ALGORITHM; ARTICLE; BASE PAIRING; CLUSTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; HISTOGRAM; IMAGE ANALYSIS; INTERNET; MATHEMATICAL COMPUTING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; STATISTICAL ANALYSIS; STRUCTURAL BIOINFORMATICS; STRUCTURE ANALYSIS; THERMODYNAMICS; THREE DIMENSIONAL IMAGING; ZYGOSACCHAROMYCES; ZYGOSACCHAROMYCES BAILI;

ZYGOSACCHAROMYCES;

EID: 27544437866     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti632     Document Type: Article

References (9)

1. Ding,Y. and Lawrence,C.E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res., 31, 7280-7301.
2. Ding,Y. et al. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res., 32 (Web Server issue), W135-W141.
3. Ding,Y. et al. (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA, 11, 1157-1166.
4. Kruskal,J.B. and Wish,M. (1977) Multidimensional Scaling. Sage Publications, Beverly Hills, CA.
5. Mathews,D.H. et al. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
6. Xia,T. et al. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37, 14719-14735.
7. Zuker,M. (1989) On finding all suboptimal foldings of an RNA molecule. Science, 244, 48-52.
8. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
9. Zuker,M. and Stiegler,P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.