:: DESCRIPTION
Triplexator (triple-helix locator) is an efficient computational framework that addresses all three aspects of triplex-formation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fabian A. Buske et al.,
“Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data“,
Genome Res, 2012, 22, 1372-1381,
:: DESCRIPTION
NASP is a computer program that will allow predict the most evolutionarily conserved secondary structures evident within a set of aligned nucleic acid sequences. It will progressively identify all of the most probable secondary structures that display some degree of sequence conservation between sequences in an analysed alignment.
::DEVELOPER
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Sep 1;27(17):2443-5. doi: 10.1093/bioinformatics/btr417. Epub 2011 Jul 14.
NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments.
Semegni JY1, Wamalwa M, Gaujoux R, Harkins GW, Gray A, Martin DP.
:: DESCRIPTION
QRNAS (Quick Refinement of Nucleic Acid Structures) is an extension of the AMBER simulation method with additional terms associated with explicit hydrogen bonds, co-planarity base pairs, backbone regularization, and custom restraints. QRNAS is capable of handling RNA, DNA, chimeras and hybrids thereof, and enables modeling of nucleic acids containing modified residues.
::DEVELOPER
Laboratory Of Bioinformatics And Protein Engineering
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM.
QRNAS: software tool for refinement of nucleic acid structures.
BMC Struct Biol. 2019 Mar 21;19(1):5. doi: 10.1186/s12900-019-0103-1. PMID: 30898165; PMCID: PMC6429776.
:: DESCRIPTION
NCBRPred is a new sequence-based computational predictor for identifying DNA-binding residues and RNA-binding residues.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhang J, Chen Q, Liu B.
NCBRPred: predicting nucleic acid binding residues in proteins based on multilabel learning.
Brief Bioinform. 2021 Sep 2;22(5):bbaa397. doi: 10.1093/bib/bbaa397. PMID: 33454744.
:: DESCRIPTION
ThermonucleotideBLAST is a software program for searching a target database of nucleic acid sequences using an assay specific query.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The NASSAM (Nucleic Acid Search for Substructures And Motifs) program searches for 3D motifs and patterns of bases in RNA (and RNA associated) PDB formatted query structures.
::DEVELOPER
The Molecular Function Regulation Lab (M. Firdaus Raih research group)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hazrina Y. Hamdani, Sri D. Appasamy, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2012.
NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules.
Nucleic Acids Research. doi: 10.1093/nar/gks513.
:: DESCRIPTION
The COGNAC server is a graph theoretical program that analyses and annotates hydrogen bonded interactions between bases in RNA 3D structures (PDB formatted).
::DEVELOPER
The Molecular Function Regulation Lab (M. Firdaus Raih research group)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures.
Firdaus-Raih M, Hamdani HY, Nadzirin N, Ramlan EI, Willett P, Artymiuk PJ.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W382-8. doi: 10.1093/nar/gku438.
:: DESCRIPTION
UNAFold (Unified Nucleic Acid Folding & Hybridization Package) is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (C(p)), and mole fractions of different molecular species are computed as a function of temperature.
mfold has been replaced by UNAFold.Although UNAFold will install without mfold_util, the sir_graph and boxplot_ng programs from the mfold_util package are required in order to obtain structure plots and dot plots from UNAFold. Install mfold_util before installing UNAFold. Versions 3.4 and higher of mfold contains all of the non-interactive programs in mfold_util, so a separate download is not required.
MFold Interface is Perl/Tk GUI Interface for Dr. Michael Zuker’s MFold.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Methods Mol Biol. 2008;453:3-31.
UNAFold: software for nucleic acid folding and hybridization.
Markham NR, Zuker M.
:: DESCRIPTION
Palingol is a declarative programming language to describe nucleic acids’ secondary structures and to scan sequence databases.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Billoud, B. Kontic, M. and Viari, A. (1996).
Palingol, a descriptive programming language to describe nucleic acid’s secondary structure and scan sequence databases.
Nucleic Acids Research 24(8) 1395-1404.
:: DESCRIPTION
Sfold predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids.Sfold is based on patent-pending algorithms developed by Ding and Lawrence (2001, 2002, 2003) for RNA folding, prediction of target accessibility, and rational design of RNA-targeting nucleic acids. The RNA folding algorithm generates a statistical sample of secondary structures from the Boltzmann ensemble of RNA secondary structures. From a statistical mechanics perspective, an RNA molecule can have a population of structures distributed according to a Boltzmann distribution, which gives the probability of a secondary structure I at equilibrium as (1/U)exp[-E(I)/RT], where E(I) is the free energy of the structure, R is the gas constant, T is the absolute temperature, and U is the partition function for all admissible secondary structures of the RNA sequence. The algorithm samples secondary structures exactly and rigorously according to the Boltzmann distribution, using recent Turner free energy rules.
::DEVELOPER
Wadsworth Bioinformatics Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ding, Y., Chan, C.Y. and Lawrence, C.E. (2005)
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble.
RNA 11, 1157-1166.
Ding, Y. and Lawrence, C.E. (2003)
A statistical sampling algorithm for RNA secondary structure prediction.
Nucleic Acids Res. 31, 7280-7301.
