:: DESCRIPTION
RECONSTRUCT is a command line program for reconstruction of protein contact maps that uses the distgeom program of the TINKER package.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Optimal contact definition for reconstruction of Contact Maps.
Jose M Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis and Michael Lappe.
BMC Bioinformatics 2010, 11:283.
:: DESCRIPTION
Rclick is capable of superimposing the RNA 3D structures by using the algorithm of clique matching and 3D least squares fitting.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rclick: A web server for comparison of RNA 3D structures.
Nguyen MN, Verma C.
Bioinformatics. 2014 Nov 12. pii: btu752.
:: DESCRIPTION
Xlink Analyzer is an interactive software for visualizing cross-links on structures and analyzing how the structures agree with the cross-links.
::DEVELOPER
Jan Kosinski kosinski@embl.de, Structural and Computational Biology Unit European Molecular Biology Laboratory (EMBL)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Struct Biol. 2015 Mar;189(3):177-83. doi: 10.1016/j.jsb.2015.01.014. Epub 2015 Feb 7.
Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures.
Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M.
:: DESCRIPTION
R3D-2-MSA enables users to select nucleotides from representative RNA 3D structures and seamlessly access sequence variants from large and diverse sequence alignments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2015 Jun 5. pii: gkv543.
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N
:: DESCRIPTION
SPOT-Struct-RNA is a sofware for RNA-binding protein prediction from 3D structure
::DEVELOPER
Laboratory of Structural Bioinformatics and Design
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2011 Apr;39(8):3017-25. doi: 10.1093/nar/gkq1266. Epub 2010 Dec 22.
Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.
Zhao H1, Yang Y, Zhou Y.
:: DESCRIPTION
The iDBPs server was developed for the identification of DNA binding proteins (DBPs) for proteins with known three-dimensional structure
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation:
Bioinformatics. 2010 Mar 1;26(5):692-3. doi: 10.1093/bioinformatics/btq019. Epub 2010 Jan 19.
iDBPs: a web server for the identification of DNA binding proteins.
Nimrod G, Schushan M, Szilágyi A, Leslie C, Ben-Tal N.
:: DESCRIPTION
PoreWalker is a fully automated method for detecting and characterizing transmembrane protein channels from their 3D structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS Comput Biol. 2009 Jul;5(7):e1000440. doi: 10.1371/journal.pcbi.1000440. Epub 2009 Jul 17.
PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
Pellegrini-Calace M, Maiwald T, Thornton JM.
:: DESCRIPTION
R3D Align is a web application for locally optimized, nucleotide to nucleotide pairwise alignments of RNA 3D structure
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.
Rahrig RR, Petrov AI, Leontis NB, Zirbel CL.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W15-21. doi: 10.1093/nar/gkt417.
:: DESCRIPTION
FR3D stands for “Find RNA 3D” and is commonly pronounced “Fred”. It was developed to find small RNA motifs (two to 20 nucleotides) in PDB files.
WebFR3D is the online version of FR3D, a suite of Matlab programs designed to search RNA 3D structures for user specified queries.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Michael Sarver; Craig L. Zirbel; Jesse Stombaugh; Ali Mokdad; Neocles B. Leontis.
FR3D: Finding Local and Composite Recurrent Structural Motifs in RNA 3D Structures,
Journal of Mathematical Biology (2008) 56:215–252.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W50-5. doi: 10.1093/nar/gkr249. Epub 2011 Apr 22.
WebFR3D–a server for finding, aligning and analyzing recurrent RNA 3D motifs.
Petrov AI1, Zirbel CL, Leontis NB.
:: DESCRIPTION
MCMC5C is a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC) approach to generate a representative sample from the posterior distribution over structures from IF data.
::DEVELOPER
: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.
Rousseau M, Fraser J, Ferraiuolo MA, Dostie J, Blanchette M.
BMC Bioinformatics. 2011 Oct 25;12:414. doi: 10.1186/1471-2105-12-414.
