Triplexator 1.3.2 – Finding Nucleic Acid Triple Helices

Triplexator 1.3.2

:: DESCRIPTION

Triplexator (triple-helix locator) is an efficient computational framework that addresses all three aspects of triplex-formation.

::DEVELOPER

Triplexator Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler 

:: DOWNLOAD

 Triplexator

:: 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,

NASP 1.5 – Nucleic Acid Structures Predictor

NASP 1.5

:: 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

CBIO

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 NASP

 :: 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.

QRNAS – software tool for Refinement of Nucleic Acid structures

QRNAS

:: 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

  • Linux / MacOsX

:: DOWNLOAD

QRNAS

:: 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.

NCBRPred – Predicting Nucleic Acid Binding Residues in Proteins based on multi-label Learning

NCBRPred

:: DESCRIPTION

NCBRPred is a new sequence-based computational predictor for identifying DNA-binding residues and RNA-binding residues.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

NCBRPred

:: 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.

ThermonucleotideBLAST 2.04 – Searching Nucleic Acid-based Assays against Sequence Databases

ThermonucleotideBLAST 2.04

:: DESCRIPTION

ThermonucleotideBLAST is a software program for searching a target database of nucleic acid sequences using an assay specific query.

::DEVELOPER

Jason D. Gans

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • C++ Compiler

:: DOWNLOAD

  ThermonucleotideBLAST

:: MORE INFORMATION

NASSAM – 3D Pattern Searching in Nucleic Acid Structures

NASSAM

:: 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

  • Web browser

:: DOWNLOAD

 NO

:: 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.

COGNAC – COnnection Tables Graphs for Nucleic ACids

COGNAC

:: 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

  • Web browser

:: DOWNLOAD

 NO

:: 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.

UNAFold 4.0 / mfold 3.6 / MFold Interface 1.18 – Nucleic Acid Folding & Hybridization Package

UNAFold 4.0 / mfold 3.6 / MFold Interface 1.18

:: 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

UNAFold team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

UNAFoldmfold , MFold Interface

:: MORE INFORMATION

Citation

Methods Mol Biol. 2008;453:3-31.
UNAFold: software for nucleic acid folding and hybridization.
Markham NR, Zuker M.

Palingol 1.3 – Programming Language in the Description of Nucleic Acids Secondary Structures

Palingol 1.3

:: DESCRIPTION

Palingol is a declarative programming language to describe nucleic acids’ secondary structures and to scan sequence databases.

::DEVELOPER

L’Atelier de BioInformatique

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Palingol

:: 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.

Sfold 2.2 – Statistical Folding and Rational Design of Nucleic Acid

Sfold 2.2

:: 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

  • Linux
  • Perl

:: DOWNLOAD

 Sfold

:: 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.