User:Wayne Decatur/Structure analysis tools

(Difference between revisions)

Revision as of 15:56, 13 July 2017

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.

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.

User:Wayne Decatur/I-Ppo Morph Methods - uses several structure analysis tools to generate a morph of a protein-nucleic acid complex

↑ 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

@@ Line 3: / Line 3: @@
 * [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.)
 * [https://biasmv.github.io/pv/ PV - JavaScript Protein Viewer]
+* [http://rasbt.github.io/biopandas/  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 [[http://rasbt.github.io/biopandas/tutorials/Working_with_PDB_Structures_in_DataFrames/ here]].
+* [http://prody.csb.pitt.edu/index.html 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.
 ===RNA===