User:Wayne Decatur/Homology Modeling: Difference between revisions

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**3D Structure

*** [http://iimcb.genesilico.pl/modernaserver/ ModeRNA server] is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. Related to this is [http://iimcb.genesilico.pl/moderna/ ModeRNA], which is a program for comparative modeling of RNA 3D structures. It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence and allows for nucleotide modifications. See the companion [http://bioinformatics.oxfordjournals.org/content/27/17/2441.short?rss=1 article] for the server.

***[http://biophy.hust.edu.cn/3dRNA/ 3dRNA] also uses templates but you don't have control in specifying it. You upload a sequence and a secondary structure and if there is a reasonable template it will run and give you the resulting model.

*Nucleic Acid-protein modeling

**The [http://iimcb.genesilico.pl/index.php/software.html software page at the Bujnicki Laboratory website] hosts software for determining two medium-resolution, knowledge-based potentials for scoring protein-RNA models obtained by docking. See the companion [http://www.biomedcentral.com/1471-2105/12/348 article].

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 **3D Structure
 *** [http://iimcb.genesilico.pl/modernaserver/ ModeRNA server] is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. Related to this is [http://iimcb.genesilico.pl/moderna/ ModeRNA], which is a program for comparative modeling of RNA 3D structures. It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence and allows for nucleotide modifications. See the companion [http://bioinformatics.oxfordjournals.org/content/27/17/2441.short?rss=1 article] for the server.
+***[http://biophy.hust.edu.cn/3dRNA/ 3dRNA] also uses templates but you don't have control in specifying it. You upload a sequence and a secondary structure and if there is a reasonable template it will run and give you the resulting model.
 *Nucleic Acid-protein modeling
 **The [http://iimcb.genesilico.pl/index.php/software.html software page at the Bujnicki Laboratory website] hosts software for determining two medium-resolution, knowledge-based potentials for scoring protein-RNA models obtained by docking. See the companion [http://www.biomedcentral.com/1471-2105/12/348 article].