RNA2D3D rev. (Beta) 5.6.3, June 14, 2011. (Linux binary; OpenGL-based GUI, with links to Tinker)RNA2D3D is an interactive software package for the conversion of 2D RNA to 3D structures. First pass conversion is based on purely geometric criteria (idealized A-form helices). Following it, the user can interactively refine the structure via such features such as H-loop shaping, helix compactification, designated helix stacking, and substitution of structure subsets with known 3D motifs (PDB). Energy minimization and short molecular dynamics runs relying on Tinker (automatically installed with kind permission of prof. J. Ponder) can be used for further refinements. Pseudoknots can be handled either automatically, or, if they are sterically very complicated, built interactively by the user. RNA2D3D can also be used to build RNA-based nano structures, such as tecto-squares and meshes (see Chworos et al.,Science 306, 2004). The system comes with a directory containing several sample structures (including pseudoknots and tecto-square building blocks) and offers help information dealing with the big picture issues as well as usage details.NOTE: Despite the rev. number 5.6.3. this version is newer and more stable than the previously designated rev. 5.7 (different development path). Due to changes in the Tinker 5.x, which are incompatible with RNA2D3D (mid 2009), we temporarily include the previous version of Tinker binaries (v. 4.2) compatible with RNA2D3D, instead of a web download (wget) at the installation time. In response to user-raised issued we stamped out the known bugs in the code. PLEASE, keep in mind that this is a research software, and not an industrial strength package.
Reference: Martinez, H., Maizel, J.V. Jr., and Shapiro, B.A. "RNA2D3D: a program for
generating, viewing, and comparing 3-dimensional models of RNA."
J Biomol Struct Dyn. 2008 Jun;25(6):669-83.Installation:
1) Download the distribution file. NOTE: Following step 2, a new subdirectory will be created.
2) Uncompress and extract the distribution files: tar -xzvf rna2d3d-file.gz
3) PLEASE, READ the RNA2D3D-README.txt file for the installation options.
4) Run C-shell (csh) script: CONFIG-RNA2D3D for the easiest installation.
5) Please, register your use of Tinker.
6) See the RNA2D3D-README.txt file for a step-by-step tectosqure building example.
RNA2D3D rev. Beta 5.7.0, May 19, 2010. (SGI/Irix binary; OpenGL-based GUI, with links to Tinker)This is the SGI MIPS / IRIX 6.5 version of the RNA2D3D package.Installation: Same as for the Linux version.
StructureLab rev. 4.5.0, Jan. 06, 2011. (Linux binary)StructureLab RNA/DNA Structure Analysis Workbench - executable files for StructureLab to be run on a Linux operating system. System configuration files appl-hosts.config and network.config are supplied along with energy tables for 4 different energy rule sets. Additional adjunct software includes binaries for RasMol and RNA2D3D (non-interactive version) with links to energy minimization via Tinker (automatically built from the source files available on the Tinker Home Page, with kind permission of prof. J. Ponder), genalign associated binaries for structural sequence alignment, binaries for RNA/DNA structural topology comparison and clustering as well as scripts which allow invocation of StructureLab from the user's local disk. Example test data is also provided as well as installation instructions.NEW: Bugs were fixed in sub-structure free energy calulators, in secondary structure window directories and in a (folding output) CT file to REG and SEQ file converter. New, expanded README.TXT file incorporates issues encountered in Ubuntu and Red Hat installations. We temporarily include the last correctly working version of Tinker binaries (v. 4.2), instead of a "live" web download (wget) at the installation time.Installation:
1) Download the distribution file into a dedicated directory.
2) Extract the distribution files: tar -xzf slab-file.gz .
3) Run shell script INSTALL-SLAB rev# (will end with a test run of StructureLab).
4) IMPORTANT: Please, read the README.TXT file for StructureLab and StructureLab/OS interface configuration issues.
5) NOTE: This binary requires that your system has libc.so.6 point/link to libc-2.3 or newer.
StructureLab rev. 4.5.0, Jan. 06, 2011. (SGI/Irix binary)StructureLab RNA/DNA Structure Analysis Workbench - executable files for StructureLab to be run on an SGI Irix 6.5 operating system. All the adjunct software packages available for Linux version are also in the SGI version, including RNA2D3D with links to Tinker.NEW: See the comments for Linux rev 4.5.0Installation: Same as for the Linux binary (please, disregard the libc information for Linux).
RSmatch2.0 - UNIX Version
The RSmatch package provides an approach to compare RNA structures, thereby uncovering functional structure elements. The software provides three different functions: 1) Pair-wise comparison and Database Search, 2) Multiple structure alignment with an extended mode to compute common structure, and 3) Iterative database search.The Vienna RNA package must be installed if sequences written in the FASTA format are used. The Vienna RNA package can be downloaded at http://www.tbi.univie.ac.at/~ivo/RNA/
. For more information, please see http://datalab.njit.edu/biodata/rna/RSmatch/software.htm
KNetFold rev. 1.4.4b (Linux binary)KNetFold v 1.4.4b executable file for the Linux operating system. A software for predicting the concensus RNA secondary structure for a given alignment of nucleotide sequences.
CorreLogo v 1.2.6, Jan. 10, 2011.A downloadable tar file contains souce files (C++) and 64-bit Linux binaries for the CorreLogo (same as our web server for the 3D sequence logos of RNA and DNA alignments).Installation:
1) Uncompress the tar file with: tar -xfz correlogo_v1.2.6.tar.gz
NanoTiler v 0.11.1 , Jun 6. 2012. Java 6 application.NanoTiler is a Java application for the design of RNA nanostructures. Among other things, it can accomplish the following: 1) Detection, extraction and annotation of RNA structural elements, 2) Use of RNA building blocks for assemblying larger structures, 3) Combinatorial search of building blocks 4) Optimization of building block positions 5) Topology classification 6) Sequence Optimization (i.e. sequence design for self-assembly into the given topology).Installation:
1) Uncompress the tar file with: tar xfz nanotiler_v0.11.1_j6.tar.gz
2) Continue by following the installation instructions in nanotiler_v0.11.1/doc/NanoTilerUserManual.pdf
CovaRNA (C++ sources) and CovStat (R package)The CovaRNA and CovStat software packages for detecting long-range covariations in nucleotide alignments. This is the software corresponding to the publication of Bindewald and Shapiro: Computational deteaction of abundant nucleotide-covariation in Drosophila genomes. RNA, 2013.Installation: unpack tar file with command tar xvfz covarna_1.16.0.tar.gz . Follow installation instructions in README file.