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Dr. Bruce A. Shapiro

We would like to hear from you about any installation and use problems, as well as no-problem experiences.

Suggestions and comments are always welcome. Please, contact Dr. Bruce A. Shapiro

Requested Software

2020/2018 VBox Virtual Machine: Ubuntu 18.04/14.04 LTS Linux, MPGAfold (18.04) Galaxy server with NanoTiler (14.04), RNA2D3D 5.6.3 and StructureLab 4.7.0 installed (~3.3 - 5.3GB VM appliance file)

MPGAfold is a Massively Parallel Genetic Algorithm for RNA/DNA secondary structure prediction, including H-type pseudoknots. Local Galaxy server with NanoTiler tools pipeline is the most user-friendly version of this flexible RNA nanostructure building software. 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 can be used for further refinements. StructureLab or SLab is an RNA/DNA Structure Analysis Workbench.

NEW: Built and tested in Oracle's VirtualBox 5.x and 6.x on MS Windows 10 and macOS 10.10 .. 10.14 host operating systems. The key advantage of this VM package is that all the non-trivial installation steps and dependencies on 64 bit and 32 bit libraries have been properly resolved.

Installation instructions are listed on the download page (next step).

Oracle's free VirtualBox package is available from http://www.virtualbox.org

2020/2017 VBox Virtual Machine: CentOS 7.7/CentOS 6.10 Linux, MPGAfold (7.7), RNA2D3D 5.6.3, and StructureLab 4.7.0 installed (~2.2 - 2.8GB VM appliance file)

MPGAfold is a Massively Parallel Genetic Algorithm for RNA/DNA secondary structure prediction, including H-type pseudoknots. 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 can be used for further refinements. StructureLab or SLab is an RNA/DNA Structure Analysis Workbench.

NEW: Built and tested in Oracle's VirtualBox 5.x and 6.x on MS Windows 10 and macOS 10.10 .. 10.14 host operating systems. The key advantage of this VM package is that all the dependencies on 64 bit and 32 bit libraries have been properly resolved. Once installed, CentOS 6.6 can be updated to version 6.10 Final.

Installation instructions are listed on the download page (next step).

Oracle's free VirtualBox package is available from http://www.virtualbox.org

2018 RiboSketch

Novel RNA/DNA drawing program for the production of secondary structure images, capable of multi-stranded molecule drawing with dynamic simulation mode for the optimization of layout and multiple interactive style and layout options.

RNA2D3D rev. 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.

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 instructions are listed on the download page (next step).

RNA2D3D rev. 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 instructions are listed on the download page (next step).

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 instructions are listed on the download page (next step).

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.

Installation instructions are listed on the download page (next step).

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.

RSmatch2.0 - WINDOWS 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.

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.

Installation instructions are listed on the download page (next step).

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 instructions are listed on the download page (next step).

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 instructions are listed on the download page (next step).

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