NOFOLD 1.0.1 – RNA Structure Clustering without Folding or Alignment

NOFOLD 1.0.1

:: DESCRIPTION

NoFold is an approach for characterizing and clustering RNA secondary structures without computational folding or alignment. It works by mapping each RNA sequence of interest to a structural feature space, where each coordinate within the space corresponds to the probabilistic similarity of the sequence to an empirically defined structure model (e.g. Rfam family covariance models).

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

NOFOLD

:: MORE INFORMATION

Citation

Middleton SA, Kim J.
NoFold: RNA structure clustering without folding or alignment.
RNA. 2014 Nov;20(11):1671-83. doi: 10.1261/rna.041913.113. Epub 2014 Sep 18. PMID: 25234928; PMCID: PMC4201820.

RNAHeliCes 2.0.14 – RNA Folding Space Analysis

RNAHeliCes 2.0.14

:: DESCRIPTION

RNAHeliCes is a tool for RNA folding space analysis. It abstracts from structural detail and maps structures using a position-specific abstraction based on helices.

::DEVELOPER

Cyanolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 RNAHeliCes

:: MORE INFORMATION

Citation:

RNA. 2012 Dec;18(12):2135-47. doi: 10.1261/rna.033548.112. Epub 2012 Oct 25.
Abstract folding space analysis based on helices.
Huang J1, Backofen R, Voß B.

BACH / BACH-MIX – Bayesian 3D constructor for Hi-C data / Characterize Structural Variations of Chromatin Folding

BACH / BACH-MIX

:: DESCRIPTION

BACH is a novel Bayesian probabilistic approach for analyzing Hi-C data. BACH takes the Hi-C contact matrix and local genomic features (restriction enzyme cutting frequencies, GC content and sequence uniqueness) as input and produces, via MCMC computation, the posterior distribution of three-dimensional (3D) chromosomal structure

BACH-MIX is an extended BACH algorithm to characterize structural variations of chromatin folding

::DEVELOPER

Jun Liu

:: SCREENSHOTS

bach

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 BACH , BACH-MIX

:: MORE INFORMATION

Citation

Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. (2013)
Bayesian Inference of Spatial Organizations of Chromosomes.
PLoS Computational Biology 9(1): e1002893.

RNAexinv – Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences

RNAexinv

:: DESCRIPTION

RNAexinv is an interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes.

::DEVELOPER

RNAexinv team

:: SCREENSHOTS

RNAexinv

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 RNAexinv

:: MORE INFORMATION

Citation

RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences.
Avihoo A, Churkin A, Barash D.
BMC Bioinformatics. 2011 Aug 3;12:319. doi: 10.1186/1471-2105-12-319.

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

MFoldInterface

:: 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.

FoldNucleus – Calculation the Folding Nucleus for RNA or Protein

FoldNucleus

:: DESCRIPTION

FoldNucleus is a server  to calculate the folding nucleus for RNA molecules with known 3D structures-including pseudoknots, tRNAs, hairpins, and ribozymes-and for protein molecules with known 3D structures, as long as they are smaller than 200 amino acid residues.

::DEVELOPER

FoldNucleus team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2015 Jun 22. pii: btv369.
FoldNucleus: Web server for the prediction of RNA and protein folding nuclei from their 3D structures.
Pereyaslavets LB, Sokolovsky IV, Galzitskaya OV.

Vfold 2.0 – RNA Structure and Folding Thermodynamics Prediction

Vfold 2.0

:: DESCRIPTION

Vfold is a software package to evaluate the stable structures and the folding free energies for RNA secondary structures and pseudoknotted structures. Recently, the Vfold model has been extended to predict loop-stem tertiary interactions in RNA pseudoknots

::DEVELOPER

Shi-Jie Chen Research Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 Vfold

:: MORE INFORMATION

Citation

Vfold: a web server for RNA structure and folding thermodynamics prediction.
Xu X, Zhao P, Chen SJ.
PLoS One. 2014 Sep 12;9(9):e107504. doi: 10.1371/journal.pone.0107504. eCollection 2014.

LatPack 1.9.1 – Folding Studies for Arbitrary Lattice Protein Models

LatPack 1.9.1

:: DESCRIPTION

LatPack is a collection of tools related to the folding simulations of lattice-protein models with arbitrary energy function.

::DEVELOPER

Bioinformatics Group
Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LatPack

:: MORE INFORMATION

Citation

HFSP J. 2008 Dec;2(6):396-404. Epub 2008 Nov 26.
Classifying proteinlike sequences in arbitrary lattice protein models using LatPack.
Mann M, Maticzka D, Saunders R, Backofen R.

pKiss 2.2.12 – Folding RNA Secondary Structures

pKiss 2.2.12

:: DESCRIPTION

pKiss is a tool for folding RNA secondary structures, including two limited classes of pseudoknots.

::DEVELOPER

Stefan Janssen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 pKiss

:: MORE INFORMATION

Citation

J Comput Biol. 2008 Mar;15(2):139-63. doi: 10.1089/cmb.2007.0198.
Novel and efficient RNA secondary structure prediction using hierarchical folding.
Jabbari H, Condon A, Zhao S.

MS2distance – Minimum Length MS2 Folding Trajectories

MS2distance

:: DESCRIPTION

MS2distance is an algorithms to compute the shortest MS2 folding trajectory between any two given RNA secondary structures.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • Python

:: DOWNLOAD

MS2distance 

:: MORE INFORMATION