Vienna+P – Modeling the interplay of Single-stranded Binding Proteins and Nucleic Acid Secondary Structure

Vienna+P

:: DESCRIPTION

Vienna+P is a tool for predicting nucleic acid secondary structure in the presence of single-stranded binding proteins, and implement it as an extension of the Vienna RNA Package.

::DEVELOPER

Ralf Bundschuh’s Statistical Physics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Vienna+P

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 1;26(1):61-7. doi: 10.1093/bioinformatics/btp627. Epub 2009 Nov 4.
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure.
Forties RA1, Bundschuh R.

NPDock – Nucleic acid-Protein Dock

NPDock

:: DESCRIPTION

NPDock is a web server for modeling of RNA-protein and DNA-protein complex structures.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NPDock: a web server for protein-nucleic acid docking.
Tuszynska I, Magnus M, Jonak K, Dawson W, Bujnicki JM.
Nucleic Acids Res. 2015 May 14. pii: gkv493

NUPARM-Plus – Analysis of Sequence Dependent Variations in Nucleic Acid Double Helices

NUPARM-Plus

:: DESCRIPTION

NUPARM-Plus is a program for analysis of sequence dependent variations in nucleic apdb_id (DNA & RNA) double helices

::DEVELOPER

Prof. Manju Bansal Lab, MBU, IISc, Bangalore, India.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Fortran

:: DOWNLOAD

NUPARM-Plus

:: MORE INFORMATION

Citation

NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures.
Bansal M, Bhattacharyya D, Ravi B.
Comput Appl Biosci. 1995 Jun;11(3):281-7.

PDBjViewer 4.4.4 – Display 3D Molecular Graphics of Proteins and Nucleic Acids

PDBjViewer 4.4.4

:: DESCRIPTION

PDBjViewer (jV, for short) is a program to display molecular graphics of proteins and nucleic acids.

::DEVELOPER

Kengo Kinoshita (Graduate School of Information SciencesTohoku University) and Haruki Nakamura (IPROsaka University)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java
  • JOGL

:: DOWNLOAD

 PDBjViewer

:: MORE INFORMATION

Citation

Bioinformatics. 2004 May 22;20(8):1329-30. Epub 2004 Feb 10.
eF-site and PDBjViewer: database and viewer for protein functional sites.
Kinoshita K, Nakamura H.

POPS* 1.6.4 – Fast and Accurate Computation of Surface Areas of Proteins and Nucleic Acids

POPS* 1.6.4

:: DESCRIPTION

POPS* (Parameter optimized surfaces) is a fast algorithm to calculate solvent accessible surface areas (SASAs) of proteins and nucleic acids at atomic (default) and residue (coarse-grained) level. Atomic and residue area parameters have been optimised versus an accurate all-atom method (Naccess). Residue areas (coarse-grained) are simulated with a single sphere centered at the C-alpha atom for amino acids and at the P atom for nucleotides.

::DEVELOPER

Franca Fraternali, Luigi Cavallo, Jens Kleinjung et al

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 POPS*

:: MORE INFORMATION

Citation:

Fraternali, F. and Cavallo, L.,
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome.
Nucleic Acids Research 30 (2002) 2950-2960

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.

ThermonucleotideBLAST 2.01 – Searching Nucleic Acid-based Assays against Sequence Databases

ThermonucleotideBLAST 2.01

:: 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

UNAFold 3.9-1 / mfold 3.6 / MFold Interface 1.18 – Nucleic Acid Folding & Hybridization Package

UNAFold 3.9-1 / 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

Professor Michael Zuker  ,Wade Schulz

:: 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.

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

The UCT Computational Biology Group

:: SCREENSHOTS

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.