User:Wayne Decatur/NASCE2011: Difference between revisions
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*See the end of [http://www.umass.edu/molvis/workshop/umass11.htm Eric Martz's recent workshop syllabus] where he covers homology (more accurately, comparative) modeling. | *See the end of [http://www.umass.edu/molvis/workshop/umass11.htm Eric Martz's recent workshop syllabus] where he covers homology (more accurately, comparative) modeling. | ||
*[http://www.biotechniques.com/news/biotechniquesNews/biotechniques-309517.html A Feb. 1st 2011 news item about Yang Zhang and his work]. | *[http://www.biotechniques.com/news/biotechniquesNews/biotechniques-309517.html A Feb. 1st 2011 news item about Yang Zhang and his work]. | ||
* Mutating an amino acid in a | * Mutating an amino acid in a protein - [http://www.pymolwiki.org/index.php/Mutagenesis here with PyMOL] and [http://spdbv.vital-it.ch/mutation_guide.html here with Swiss PDB-Viewer] | ||
*Homology modeling | *Homology modeling | ||
**[http://www.umass.edu/molvis/workshop/homolmod.htm Eric Martz's page on Homology Modeling] | **[http://www.umass.edu/molvis/workshop/homolmod.htm Eric Martz's page on Homology Modeling] | ||
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**[http://zhanglab.ccmb.med.umich.edu/QUARK/ Quark server] | **[http://zhanglab.ccmb.med.umich.edu/QUARK/ Quark server] | ||
**[http://www.ks.uiuc.edu/Research/vmd/ VMD - Visual Molecular Dynamics] | **[http://www.ks.uiuc.edu/Research/vmd/ VMD - Visual Molecular Dynamics] | ||
*RNA modeling | |||
**Secondary Structure | |||
*** The [http://iimcb.genesilico.pl/comparna/methods/ methods page for CompaRNA] lists and provides links to several software and server-based programs for secondary structure prediction. | |||
*** [http://web.cbio.uct.ac.za/~yves/nasp/ NASP] is a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments. See the companion [http://bioinformatics.oxfordjournals.org/content/27/17/2443.short?rss=1 article]. | |||
**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 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. | |||
*RNA-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]. | |||
==Class Sandboxes== | ==Class Sandboxes== | ||
