User:Wayne Decatur/Structure analysis tools
From Proteopedia
- 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
- BioPandas - "Working with molecular structures in pandas DataFrames". Combining Python, Pandas, and Structural data awesomely. Has nice PDB parser that lets you get whole header, for example see [here].
- ProDy Project - "ProDy is a free and open-source Python package for protein structural dynamics analysis". Looks like it does protein sequence analysis too and working with PDB files.
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 and a 2017 article on it here[3].
- RNApdbee -a webserver to derive secondary structures from PDB files of knotted and unknotted RNAs PMID: 24771339[4]. Use it here.
Mutations
Related
- User:Wayne Decatur/I-Ppo Morph Methods - uses several structure analysis tools to generate a morph of a protein-nucleic acid complex
- S. cerevisiae complexes
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
- ↑ Hanson RM, Lu XJ. DSSR-enhanced visualization of nucleic acid structures in Jmol. Nucleic Acids Res. 2017 May 3. doi: 10.1093/nar/gkx365. PMID:28472503 doi:http://dx.doi.org/10.1093/nar/gkx365
- ↑ 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
