Paper Info
Title
Dihedral-Based Segment Identification and Classification of Biopolymers II: Polynucleotides.
Abstract
In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers I: Proteins. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400541d), we introduce a new algorithm for structure classification of biopolymeric structures based on main-chain dihedral angles. The DISICL algorithm (short for Dihedral-based Segment Identification and CLassification) classifies segments of structures containing two central residues. Here, we introduce the DISICL library for polynucleotides, which is based on the dihedral angles e, C, and x for the two central residues of a three-nucleotide segment of a single strand. Seventeen distinct structural classes are defined for nucleotide structures, some of which to our knowledge were not described previously in other structure classification algorithms. In particular, DISICL also classifies noncanonical single-stranded structural elements. DISICL is applied to databases of DNA and RNA structures containing 80,000 and 180,000 segments, respectively. The classifications according to DISICL are compared to those of another popular classification scheme in terms of the amount of classified nucleotides, average occurrence and length of structural elements, and pairwise matches of the classifications. While the detailed classification of DISICL adds sensitivity to a structure analysis, it can be readily reduced to eight simplified classes providing a more general overview of the secondary structure in polynucleotides.
Year
DOI
Venue
2014
10.1021/ci400542n
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Keywords
DocType
Volume
computational biology,polynucleotides,algorithms,computer simulation,hydrogen bonding,proteins
Journal
54
Issue
ISSN
Citations 
1
1549-9596
2
PageRank 
References 
Authors
0.48
9
2
Name
Order
Citations
PageRank
Gabor Nagy133620.76
Chris Oostenbrink229738.41