Nucleic Acids

SBGrid supports 10 nucleic acids software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

3DNA

- a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun ...

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  • a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun Lu in the laboratory of Professor Wilma K. Olson at the Department of Chemistry and Chemical Biology, Rutgers-the State University of New Jersey.

Developers

Wilma Olson

Xiang-Jun Lu

Categories

X-ray Crystallography

Structure Analysis

Structure Visualization

Nucleic Acids

Versions

Citations

Xiang-Jun Lu and Wilma K Olson (2008) "3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures." Nature Protocols, 3, 1213-1227.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid 3DNA page.

AMIGOS II

- allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific ...

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  • allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures. AMIGOS II was authored by Leven Wadley in the lab of Anna Marie Pyle at Yale University.

Developers

Amelia Johnson

Anna Pyle

Levan Wadley

Kevin Keating

Categories

Nucleic Acids

Versions

Citations

Duarte and Pyle. Stepping through an RNA structure: A novel approach to conformational analysis. J Mol Biol. 1998. 284(5):1465-78.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid AMIGOS II page.

CURVES

- an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to ...

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  • an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis.

Developers

Richard Lavery

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Lavery and Sklenar. Defining the structure of irregular nucleic acids: conventions and principles. J Biomol Struct Dyn (1989) vol. 6 (4) pp. 655-67

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid CURVES page.

Curves+

- a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the ...

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  • a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the helper programs Canal, Cdif and Sumr.

Developers

Richard Lavery

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Lavery et al. Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res (2009) vol. 37 (17) pp. 5917-29

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid Curves+ page.

ENTANGLE

- a JAVA program that reads PDB files containing a nucleic-acid protein complex and gives a listing of ...

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  • a JAVA program that reads PDB files containing a nucleic-acid protein complex and gives a listing of interactions that occur at the interface between the nucleic-acid/protein complex. These interactions are then classified into hydrogen bonds, electrostatic, hydrophobic, and Van der Waals. Entangle also recognizes when a stacking interaction occurs between two aromatic residues. In addition to a listing, Entangle allows the user to probe the interface in three-dimensions.

Developers

Yousif Shamoo

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Allers and Shamoo. Structure-based analysis of protein-RNA interactions using the program ENTANGLE. Journal of molecular biology (2001) vol. 311 (1) pp. 75-86

Technical Notes

Not all PDBs work with this program.

Some example PDBs that work:
1URW
1CVJ

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid ENTANGLE page.

Madbend

- a program for calculating the curvature of nucleic acids. From a given list of base pair step ...

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  • a program for calculating the curvature of nucleic acids. From a given list of base pair step roll, tilt and twist values, and the specification of a reference plane, the program produces the global tilt, global roll and the bend magnitude. These quantities thus describe the direction and magnitude of a bend angle and can be used to analyze DNA and DNA/protein complex geometries.

Developers

Dan Strahs

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Barbic and Crothers. Comparison of analyses of DNA curvature. J Biomol Struct Dyn (2003) vol. 21 (1) pp. 89-97

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid Madbend page.

NUCCYL

- a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified ...

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  • a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.

Developers

Luca Jovine

Categories

Structure Visualization

Nucleic Acids

Versions

Citations

There is no paper describing nuccyl (yet). However, if you found the program useful and would like to mention it in your publications together with PyMOL, you could use an URL citation of the type:

Jovine, L. nuccyl (2003) http://www.biosci.ki.se/groups/ljo/software/nuccyl.html

License Type

This software is distributed under an Open license.


Static link to the SBGrid NUCCYL page.

NUCPLOT

- a program to generate schematic diagrams of protein-DNA interactions. The program works for any single- or double-stranded ...

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  • a program to generate schematic diagrams of protein-DNA interactions. The program works for any single- or double-stranded protein-DNA, DNA-ligand and protein-RNA complexes.

Developers

Roman Laskowski

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Luscombe N M, Laskowski R A, Thornton J M. NUCPLOT: a program to generate schematic diagams of protein-DNA interactions. Nucleic Acids Research. 1997. 25:4940-4945.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid NUCPLOT page.

RCrane

- allows for semi-automated building of RNA structure within Coot.

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  • allows for semi-automated building of RNA structure within Coot.

Developers

Kevin Keating

Categories

X-ray Crystallography

Nucleic Acids

Versions

Citations

Keating and Pyle. Semiautomated model building for RNA crystallography using a directed rotameric approach. Proc Natl Acad Sci USA (2010) vol. 107 (18) pp. 8177-82

License Type

This software is distributed under an Open license.


Static link to the SBGrid RCrane page.

RNAView

- a program is developed to quickly display the secondary structure of RNA/DNA with tertiary interactions. It is ...

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  • a program is developed to quickly display the secondary structure of RNA/DNA with tertiary interactions. It is fully implemented with Leontis and Westhof's ( RNA (2001) 7, 499-512), convention for the edge-to-edge hydrogen bonding interactions.

Developers

RNAVIEW Developer Group

Categories

Structure Analysis

Nucleic Acids

Versions

Citations

Yang et al. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 2003. 31(13):3450-60

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid RNAView page.