NOTE: This project is still under construction.
We attach spin labels onto specific pairs of residues in a protein to study its conformational change. This set of programs takes a PDB ID of a protein as an input and returns a text file that contains all possible pairs of amino acid residues onto which spin labels can be attached. TL;DR: download all source codes and run main.py.
Selenium (Make sure Google Chrome is properly installed)
Requests
Biopython
Numpy
In a protein, amino acid residues onto which a spin label can be attached have the following characteristics:
- Found on secondary structure
- Not affiliated to membrane
- Not conserved
From the residues that satisfy the above three criteria, we select pairs where the distance between two residues are in an appropriate range.
When main.py is run, the user is asked for the PDB ID of a protein, and these criteria are checked by the DSSPRunner class defined in dssp_runner.py, the TopconsRunner class defined in topcons_runner.py, and the ConsurfRunner class defined in consurf_runner.py, respectively, and the results are stored in a Protein object constructed based on the protein the user provided.
After getting a set of qualified residues, the distances between each pair of residue are calculated, and the qualified pairs are displayed.
Thank the Mchaourab Lab of Vanderbilt University, especially Julia, Richard, Kevin and Hassane for their generous instructions on Bioinformatics. Thank former lab member Diego for his effort on the MMseqs2Runner class.
Thank brianshan974 for his thoughtful advice on programming.
Thanks to the scholars who have been contributing to the Computational Biology world.
Please read the headers of the programs to see details.
Ashkenazy H., Abadi S., Martz E., Chay O., Mayrose I., Pupko T., and Ben-Tal N. 2016
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecule
Nucl. Acids Res. 2016; DOI: 10.1093/nar/gkw408; PMID: 27166375
Celniker G., Nimrod G., Ashkenazy H., Glaser F., Martz E., Mayrose I., Pupko T., and Ben-Tal N. 2013.
ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function
Isr. J. Chem. 2013 March 10, doi: 10.1002/ijch.201200096
Ashkenazy H., Erez E., Martz E., Pupko T. and Ben-Tal N. 2010
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
Nucl. Acids Res. 2010; DOI: 10.1093/nar/gkq399; PMID: 20478830
Landau M., Mayrose I., Rosenberg Y., Glaser F., Martz E., Pupko T. and Ben-Tal N. 2005.
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures.
Nucl. Acids Res. 33:W299-W302.
Glaser F., Pupko T., Paz I., Bell R.E., Bechor D., Martz E. and Ben-Tal N. 2003.
ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information.
Bioinformatics 19:163-164.
A series of PDB related databases for everyday needs.
Wouter G Touw, Coos Baakman, Jon Black, Tim AH te Beek, E Krieger, Robbie P Joosten, Gert Vriend.
Nucleic Acids Research 2015 January; 43(Database issue): D364-D368.
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
Kabsch W, Sander C, Biopolymers. 1983 22 2577-2637.
PMID: 6667333; UI: 84128824.
Clustering huge protein sequence sets in linear time
https://doi.org/10.1038/s41467-018-04964-5
MMseqs2 enables sensitive protein sequence searching for the analysis
of massive data sets"
https://doi.org/10.1038/nbt.3988
Madeira F, Pearce M, Tivey ARN, et al.
Search and sequence analysis tools services from EMBL-EBI in 2022.
Nucleic Acids Research. 2022 Apr:gkac240.
DOI: 10.1093/nar/gkac240. PMID: 35412617; PMCID: PMC9252731.
The TOPCONS web server for combined membrane protein topology and signal peptide prediction.
Tsirigos KD*, Peters C*, Shu N*, Käll L and Elofsson A (2015) Nucleic Acids Research 43 (Webserver issue), W401-W407.