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Demos

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Aug 8, 2010
Generating a random unfolded structure from primary sequence and secondary structure

Aug 8, 2010
Adding tertiary contact information to a random unfolded model

Aug 8, 2010
Rotating the final structure from Part B

May 5, 2010
Movie demonstrating the random unfold method

NAST paper documents

Large Structure Files

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Jun 6, 2008
Connects the residues in VMD

Jun 6, 2008
Coarse-grain (C3* atoms), with missing loop added by NAST

Jun 6, 2008
Coarse-grain version containing only C3* atoms

Jun 6, 2008
Connects the residues in VMD

Aug 8, 2011
Coarse grain version of the T. thermophilus crystal structure

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

Jun 6, 2008
Connects the residues in VMD

Jun 6, 2008
Coarse-grain (C3* atoms), with missing loop added by NAST

P4-P6 files

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Jun 6, 2008
Calculated with nucleotide radius = 4.5 Ang and solvent radius = 1.5 Ang

Jun 6, 2008
Contains only C3* atoms of the P4-P6 (1GID) crystal structure

Jun 6, 2008
Connects the residues in VMD

tRNA files

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Jun 6, 2008
Contains only C3* atoms of the tRNA (6TNA) crystal structure

Jun 6, 2008
Connects the residues in VMD

Jun 6, 2008
Calculated with nucleotide radius = 4.5 Ang and solvent radius = 1.5 Ang

Special Files

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

Feb 2, 2010
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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Jan 1, 2010
Old Numeric python module

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