title: RNABP COGEST: a resource for investigating functional RNAs.
abstract: Structural bioinformatics of RNA has evolved mainly in response to the rapidly accumulating evidence that non-(protein)-coding RNAs (ncRNAs) play critical roles in gene regulation and development. The structures and functions of most ncRNAs are however still unknown. Most of the available RNA structural databases rely heavily on known 3D structures, and contextually correlate base pairing geometry with actual 3D RNA structures. None of the databases provide any direct information about stabilization energies. However, the intrinsic interaction energies of constituent base pairs can provide significant insights into their roles in the overall dynamics of RNA motifs and structures. Quantum mechanical (QM) computations provide the only approach toward their accurate quantification and characterization. 'RNA Base Pair Count, Geometry and Stability' (http://bioinf.iiit.ac.in/RNABPCOGEST) brings together information, extracted from literature data, regarding occurrence frequency, experimental and quantum chemically optimized geometries, and computed interaction energies, for non-canonical base pairs observed in a non-redundant dataset of functional RNA structures. The database is designed to enable the QM community, on the one hand, to identify appropriate biologically relevant model systems and also enable the biology community to easily sift through diverse computational results to gain theoretical insights which could promote hypothesis driven biological research.
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India.
authors.forename: Sohini
authors.initials: S
authors.lastname: Bhattacharya
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India.
authors.forename: Shriyaa
authors.initials: S
authors.lastname: Mittal
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India.
authors.forename: Swati
authors.initials: S
authors.lastname: Panigrahi
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India.
authors.forename: Purshotam
authors.initials: P
authors.lastname: Sharma
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India.
authors.forename: Preethi
authors.initials: P
authors.lastname: S P
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India.
authors.forename: Rahul
authors.initials: R
authors.lastname: Paul
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India.
authors.forename: Sukanya
authors.initials: S
authors.lastname: Halder
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India.
authors.forename: Antarip
authors.initials: A
authors.lastname: Halder
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India.
authors.forename: Dhananjay
authors.initials: D
authors.lastname: Bhattacharyya
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India.
authors.forename: Abhijit
authors.initials: A
authors.lastname: Mitra
mesh_terms: D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D009690:Nucleic Acid Conformation; D020871:RNA Stability; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics
chemical_list: D022661:RNA, Untranslated