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Requested Software

NanoTiler, v 0.9.2 , Sep 20. 2008. 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 block combinations 4) Optimization of building block positions 5) Topology classification 6) Sequence Optimization.

Installation: 1) Uncompress the tar file with: tar xfz nanotiler_v0.9.2_j6_64.tar.gz 2) Continue by following the installation instructions in nanotiler_v0.9.2/doc/NanoTilerUserManual.pdf

RNA2D3D rev. 5.6.2, Oct. 15, 2009. (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 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 from the Tinker Home Page, 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.

NEW: Due to changes in one of the Tinker modules (mid 2009), which produces wrong pdb output format and leads to the whole system crashing, we temporarily include the last version of Tinker binaries correctly working with RNA2D3D, instead of a "live" web download at the installation time. In response to user-raised issued we stamped out the known bugs in the code. 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 into a dedicated directory. 2) Uncompress and extract the distribution files: tar -xzf rna2d3d-file.gz 3) See the RNA2D3D-README.txt file for the installation options. 4) Run shell 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. 5.6.1, Aug.28, 2008. (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. 4.4.0, Oct. 15, 2009. (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: Communications via ssh has been made more robust. Time-consuming energy calculating functions are turnrd off by default for large secondary structures (> 1,000nt) at their drawing time. Energy can be calculated via an explicit request. Keep in mind that for structures in the 7K-10K nt range calculations may take ~1 minute! New, expanded README.TXT file incorporates issues raised by the users. Due to changes in one of the Tinker modules (used by RNA2D3D), which produces wrong pdb output format, we temporarily include the last correctly working version of Tinker binaries, instead of a "live" web download 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 README.TXT for StructureLab and StructureLab/OS interface configuration issues. 5) NOTE: This binary requires that your system has libc.so.6 point to libc-2.3 or newer.

StructureLab rev. 4.4.0, Oct. 15, 2009. (SGI/Irix binary)

StructureLab RNA/DNA Structure Analysis Workbench - executable files for StructureLab to be run on an SGI-IRIX operating system. All the adjunct software packages available for Linux version is also in the SGI version, including RNA2D3D with links to Tinker.

NEW: Option of dumping StructureLab windows directly to the most popular image format files (TIF,JPG,PNG,GIF,PS,etc) has been added.

Installation: Same as for the Linux binary.

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.

RSmatch2.0 - WINDOWS Version

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.

Intended Use of Software

License Agreement

			NATIONAL INSTITUTES OF HEALTH

SOFTWARE TRANSFER AGREEMENT
This Software Transfer Agreement ("STA") has been adopted for use by the National Institutes of Health ("NIH") in all transfers of research software ("Software") whether NIH is identified below as Provider or Recipient. 
Provider: National Cancer Institute 
WHEREAS, Provider has certain proprietary software and associated material described above (hereinafter, collectively referred to as "Software") and Provider agrees to transfer such Software to Recipient's investigator, to be used solely in connection with the research project described in the web form.

NOW, THEREFORE, in consideration of the premises and mutual covenants contained herein, the Provider and Recipient agree as follows: 

1. SOFTWARE MAY NOT BE USED FOR TREATING OR DIAGNOSING HUMAN SUBJECTS. Recipient will not license or sell or use Software for commercial purposes or applications. Recipient's investigator shall retain control over Software and further will not transfer the Software to individuals not under Recipient investigator's direct supervision without express advance written approval of Provider. Recipient agrees to comply with all Federal regulations applicable to research projects and handling of research materials. 
2. Recipient agrees to use Software at single location, (hereinafter "Site") as described on web form. 
Recipient agrees not to copy Software, in whole or in part, except as required for use by Recipient's investigator at the designated Site for the Project defined in this Agreement. 
3. In all oral presentations or written publications concerning the Project, Recipient will acknowledge Provider's contribution of Software unless requested otherwise. Recipient may publish or otherwise publicly disclose the results of the Project, but if Provider has given confidential information to Recipient, such public disclosure may be made only after Provider has had 30 days to review the proposed disclosure, except when a shortened time period under court order or the Freedom of Information Act pertains. 
4. Title in the Software shall remain with the Provider. It is understood that nothing herein shall be deemed to constitute, by implication or otherwise, the grant to either Party by the other of any license or other rights under any patent, patent application or other intellectual property right or interest. Provider reserves the right to distribute Software to others and to use it for Provider's own purposes. 
5. When the Project is terminated, completed or when three (3) years have elapsed, whichever occurs first, Recipient will destroy or otherwise dispose of Software and all copies of Software as directed by Provider. Recipient will dispose of Provider's confidential information as directed by the Provider. 
6. This Agreement may be terminated by either Recipient or Provider on 30 days notice. 
7. General reports regarding the application of the Software would be appreciated and should be forwarded to the Provider. The general report should outline the effectiveness and problems encountered in using the Software, without disclosing the Recipient's confidential information. The information from the general reports may be used by Provider to enhance the capabilities of the Software. 
8. The Provider and Recipient each shall retain title to any patent or other intellectual property of their respective employees developed or created in the course of the Project defined in this Agreement. Neither Provider nor Recipient promise rights in advance for inventions developed under this Agreement. 
9. When Provider is NIH: Recipient agrees to hold the United States Government harmless and to indemnify the Government for all liabilities, demands, damages, expenses and losses arising out of Recipient's use for any purpose of Software. Recipient agrees not to claim, infer, or imply Governmental endorsement of the Project, the Recipient or Recipient's personnel conducting the Project or any resulting product(s). 
When Recipient is NIH: It is the intention of the NIH that Provider not be liable to NIH for any claims or damages arising from NIH's use of Software; however, no indemnification is provided or intended. 
10. Software is supplied AS IS, without any accompanying services or improvements from Provider. SOFTWARE IS SUPPLIED TO RECIPIENT WITH NO WARRANTIES, EXPRESS OR IMPLIED, INCLUDING ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Provider makes no representations that the use of Software will not infringe any patent or proprietary rights of third parties. 
11. The illegality or invalidity of any provision of this Agreement shall not impair, affect or invalidate the other provisions of this Agreement. 
12. The construction, validity, performance and effect of this Agreement shall be governed by Federal law, as applied by the Federal Courts in the District of Columbia. 
13. Provider, indicate if Software is Year 2000 compliant: Yes 

Provider: The National Cancer Institute

Dr. Bruce A. Shapiro, Principal Investigator


Any questions concerning legal issues should be addressed to:

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Technology Transfer Branch
National Cancer Institute
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FAX: (301) 846-6820



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