STRUCTURE OF DNA 1. primary structure 2. secondary structure 3. tertiary structure
R ESEARCH U PDATE ON J ULY 17 TH – A MY (1) Found tools for RNA tertiary structure prediction From...
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RESEARCH UPDATE ON JULY 17 TH – AMY(1) Found tools for RNA tertiary structure prediction From secondary structure to tertiary structure o NAST(2009): It cannot automatically detect tertiary structure interactions, but performs well on tRNA and P4 – P6 region in group I intron. Input: secondary structure and tertiary contact predictions. Output: 3D structure. Ref: http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2648710&blobtype=pdf o RNA2D3D(2008): It provides functions for generate, view and compare 3D RNA structures. Input: secondary structure; known fragments. Output: 3D structure o MC-Sym(2007): It forms a automatic 3D structure prediction pipeline along with MC-Fold program. Input: secondary structure; distance torsion and other structural constraints; database of known fragments. Output: series of 3D structure candidates. o S2S: Its outputs are multiple alignments, that is interesting. Input: 3D structure. Output: Multiple alignments.
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R ESEARCH U PDATE ON J ULY 17 TH – A MY (3) To make some of the found tools work Some programs lack the instructions or an elaborate readme file that make it hard to find out the input file format. Some programs are locked, and cannot be free used. To keep on finding new tools for 3D structure prediction To keep working on RNAPASTA
Transcript of R ESEARCH U PDATE ON J ULY 17 TH – A MY (1) Found tools for RNA tertiary structure prediction From...
RESEARCH UPDATE ON JULY 17TH – AMY(1) Found tools for RNA tertiary structure prediction
From secondary structure to tertiary structureo NAST(2009): It cannot automatically detect tertiary structure interactions, but
performs well on tRNA and P4 – P6 region in group I intron.Input: secondary structure and tertiary contact predictions.Output: 3D structure.Ref: http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2648710&blobtype=pdf
o RNA2D3D(2008): It provides functions for generate, view and compare 3D RNA structures.Input: secondary structure; known fragments.Output: 3D structure
o MC-Sym(2007): It forms a automatic 3D structure prediction pipeline along with MC-Fold program. Input: secondary structure; distance torsion and other structural constraints; database of known fragments.Output: series of 3D structure candidates.
o S2S: Its outputs are multiple alignments, that is interesting.Input: 3D structure.Output: Multiple alignments.
RESEARCH UPDATE ON JULY 17TH – AMY(2)
RNA 3D Structure Prediction: (1) Assessing RNA 3D Structure Similarity from 2D Structure Similarity(2004): It first generates secondary structures from known tertiary structures in databases and forms 2D databases, then compares the query secondary structure with 2D databases to find the most similar ones as to get the 3D structure of the query.Ref: http://www.jsbi.org/journal/GIW04/GIW04F012.pdfInput: 3D structures in databases; secondary structure.Output: 3D structure.
RESEARCH UPDATE ON JULY 17TH – AMY(3) To make some of the found tools work
Some programs lack the instructions or an elaborate readme file that make it hard to find out the input file format.
Some programs are locked, and cannot be free used.
To keep on finding new tools for 3D structure prediction
To keep working on RNAPASTA
