NAST (The Nucleic Acid Simulation Tool)
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Demos

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NAST Demo Part A
Aug 8, 2010
Author: Magdalena Jonikas
Generating a random unfolded structure from primary sequence and secondary structure

NAST Demo Part B
Aug 8, 2010
Author: Magdalena Jonikas
Adding tertiary contact information to a random unfolded model

NAST Demo Part C
Aug 8, 2010
Author: Magdalena Jonikas
Rotating the final structure from Part B

Random Unfold Demo
May 5, 2010
Author: Magdalena Jonikas
Movie demonstrating the random unfold method

NAST paper documents

Large Structure Files

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Azoarcus (1ZZN) PSF file
Jun 6, 2008
Author: Magdalena Jonikas
Connects the residues in VMD

Azoarcus (1ZZN) refined structure
Jun 6, 2008
Author: Magdalena Jonikas
Coarse-grain (C3* atoms), with missing loop added by NAST

Michel-Westhof Model of T. thermophilus group I intron
Jun 6, 2008
Author: Magdalena Jonikas
Coarse-grain version containing only C3* atoms

PSF file for Michel-Westhof model
Jun 6, 2008
Author: Magdalena Jonikas
Connects the residues in VMD

T. thermophilus coarse grain crystal structure
Aug 8, 2011
Author: Magdalena Jonikas
Coarse grain version of the T. thermophilus crystal structure

T. thermophilus NAST model
Aug 8, 2011
Author: Magdalena Jonikas
Coarse grain model of T. thermophilus using data from both the crystal structure and the Michel-Westof model

Twort (1Y0Q) PSF file
Jun 6, 2008
Author: Magdalena Jonikas
Connects the residues in VMD

Twort (1Y0Q) refined structure
Jun 6, 2008
Author: Magdalena Jonikas
Coarse-grain (C3* atoms), with missing loop added by NAST

P4-P6 files

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P4-P6 (1GID) solvent accessibility profile
Jun 6, 2008
Author: Magdalena Jonikas
Calculated with nucleotide radius = 4.5 Ang and solvent radius = 1.5 Ang

P4-P6 coarse-grain crystal structure
Jun 6, 2008
Author: Magdalena Jonikas
Contains only C3* atoms of the P4-P6 (1GID) crystal structure

P4-P6 PSF file
Jun 6, 2008
Author: Magdalena Jonikas
Connects the residues in VMD

tRNA files

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tRNA (6TNA) coarse-grain crystal structure
Jun 6, 2008
Author: Magdalena Jonikas
Contains only C3* atoms of the tRNA (6TNA) crystal structure

tRNA (6TNA) PSF file
Jun 6, 2008
Author: Magdalena Jonikas
Connects the residues in VMD

tRNA (6TNA) solvent accessibility profile
Jun 6, 2008
Author: Magdalena Jonikas
Calculated with nucleotide radius = 4.5 Ang and solvent radius = 1.5 Ang

Special Files

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c2a.py
Feb 2, 2010
Author: Magdalena Jonikas
Updated c2a.py file, important for end pieces of length 1

simplePdb.py
Feb 2, 2010
Author: Magdalena Jonikas
File to reduce the precision of residue positions for large RNA molecules

ZZArchive

ALL FILES

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NAST Examples

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P4-P6

Experimental Standard

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Ideal Standard

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Native Secondary Structure

Experimental Standard

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Ideal Standard

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Predicted Secondary Structure

Experimental Standard

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Ideal Standard

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tRNA files

Experimental Standard

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Ideal Standard

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T.Thermophila Group I Intron

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Uncategorized Submissions

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Numeric python module
Jan 1, 2010
Author: Magdalena Jonikas
Old Numeric python module

6,515

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Last updated
Oct 11, 2017

SimTK is maintained through Grant R01GM124443 01A1 from the National Institutes of Health (NIH). It was initially developed as part of the Simbios project funded by the NIH as part of the NIH Roadmap for Medical Research, Grant U54 GM072970.

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