:: DESCRIPTION
PDBjViewer (jV, for short) is a program to display molecular graphics of proteins and nucleic acids.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
NPDock is a web server for modeling of RNA-protein and DNA-protein complex structures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: DESCRIPTION
nuccyl is a Perl program that allows PyMOL, a powerful open-source molecular modeling system, to display atomic models of nucleic acids in a highly simplified representation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments. Many software packages for sequence alignment and the construction of evolutionary trees have implemented their own standard of saving and reading sequence alignments. To circumvent the labourious work of manually converting alignment formats with the use of a word processor, this program was written: it converts these formats automatically.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Raes, J. and Van de Peer,Y. (1999)
ForCon : a software tool for the conversion of sequence alignments.
EMBnet.news 6(1).
:: DESCRIPTION
NUCPLOT is a program that automatically generates schematic 2D representations of protein-nucleic acid interactions. The input is a standard PDB file and the output is a colour or black-and-white PostScript file which gives a simple, at-a-glance representation of the hydrogen bonds and hydrophobic contacts between proteins and nucleic acids.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Luscombe N M, Laskowski R A, Thornton J M. (1997).
NUCPLOT: a program to generate schematic diagams of protein-DNA interactions.
Nucleic Acids Research, 25, 4940-4945.
:: DESCRIPTION
NAST (Nucleic Acid Simulation Toolkit) is a knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on:
1. primary sequence
2. known or predicted secondary structure
3. known or predicted tertiary contacts (optional)
Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB.
Coarse-grained modeling of large RNA molecules with knowledge-based potentialsand structural filters.
RNA. 2009 Feb;15(2):189-99.PMID: 19144906 (2009)
