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User:Wayne Decatur/Structure analysis tools
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* [https://bhapp.c2b2.columbia.edu/PrePPI/ PrePPI]: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human. | * [https://bhapp.c2b2.columbia.edu/PrePPI/ PrePPI]: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human. | ||
* [http://ffas.burnham.org/XtalPred-cgi/xtal.pl XtalPred] - Prediction of Protein Crystallizability (program described by ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220968/ this paper by Mizianty et al. entitled "Covering complete proteomes with X-ray structures: a current snapshot."]<ref>PMID:25372670 </ref>, supposed to be better but I couldn't find a link to a webserver running it. Or anything of it online yet.) | * [http://ffas.burnham.org/XtalPred-cgi/xtal.pl XtalPred] - Prediction of Protein Crystallizability (program described by ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220968/ this paper by Mizianty et al. entitled "Covering complete proteomes with X-ray structures: a current snapshot."]<ref>PMID:25372670 </ref>, supposed to be better but I couldn't find a link to a webserver running it. Or anything of it online yet.) | ||
| + | * [ PV - JavaScript Protein Viewer](https://biasmv.github.io/pv/) | ||
===RNA=== | ===RNA=== | ||
Revision as of 19:24, 5 July 2016
- Superpose from the University of Alberta -a protein superposition server.
- PrePPI: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.
- XtalPred - Prediction of Protein Crystallizability (program described by (this paper by Mizianty et al. entitled "Covering complete proteomes with X-ray structures: a current snapshot."[1], supposed to be better but I couldn't find a link to a webserver running it. Or anything of it online yet.)
- [ PV - JavaScript Protein Viewer](https://biasmv.github.io/pv/)
Contents |
RNA
- DSSR -(Dissecting the Spatial Structure of RNA), an integrated and automated tool for analyzing and annotating RNA tertiary structures. PMID: 26184874 [2] (Maybe name of given supplemental data file previously DSSR stood for "DSSR_ a software program for Defining the Secondary Structures of RNA from three-dimensional coordinates".? Jmol now has integrated real time updates to data generated by DSSR, see here
- RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs PMID: 24771339[3].
Related
- User:Wayne Decatur/I-Ppo Morph Methods - uses several structure analysis tools to generate a morph of a protein-nucleic acid complex
References
- ↑ Mizianty MJ, Fan X, Yan J, Chalmers E, Woloschuk C, Joachimiak A, Kurgan L. Covering complete proteomes with X-ray structures: a current snapshot. Acta Crystallogr D Biol Crystallogr. 2014 Nov;70(Pt 11):2781-93. doi:, 10.1107/S1399004714019427. Epub 2014 Oct 23. PMID:25372670 doi:http://dx.doi.org/10.1107/S1399004714019427
- ↑ Lu XJ, Bussemaker HJ, Olson WK. DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Res. 2015 Dec 2;43(21):e142. doi: 10.1093/nar/gkv716. Epub 2015 Jul, 15. PMID:26184874 doi:http://dx.doi.org/10.1093/nar/gkv716
- ↑ Antczak M, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, Szachniuk M. RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W368-72. doi:, 10.1093/nar/gku330. Epub 2014 Apr 25. PMID:24771339 doi:http://dx.doi.org/10.1093/nar/gku330
