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MCPath: Monte Carlo (MC) path generation approach to predict likely allosteric pathways and functional residues

    The MCPath server http://safir.prc.boun.edu.tr/clbet_server is based on MC path generation runs with a PDB ID or an uploaded structure for:

    A) Generating paths starting from a given residue and number of steps User needs to give the initial residue index and chain ID, and the path length:

     

    Output: The output lists all pathways ranked with their probabilities and populated pathways. The top three populated pathways are displayed on the structure. The order of residues are the same with the occurence in the pathway. The residues on populated pathways are listed and colored as red. The structure is mapped as a cartoon.

    Suggestion: Selecting a central residue from ligand binding site as given residue and a proper path length varying with respect to the size of protein structure result in realistic results.

    B) Generating paths between two given residues: User needs to specify the residue index and chain ID for both initial and final residues.

     

    Output: The output lists all pathways ranked with their probabilities and populated pathways.The top three populated pathways are displayed on the structure. The order of residues are the same with the occurence in the pathway. The residues on populated pathways are listed and colored as red. The structure is mapped as a cartoon.

    Suggestion: Selecting a central residue from ligand binding site as a starting point and choosing a distal allosteric site as an end point procures possible signaling paths, as well as repeating the exercise for other binding residues.

    C) Generating a long path with an infinite number of steps for the graph centrality parameters closeness and betweenness. User needs to give the path length.

     

    Output: The residue closeness and betweenness values are provided in text files and plotted. The suggested functional residues based on the closeness and betweenness values are listed and displayed on the structure. The listed residues are colored as red on structure.

    • If an e-mail address is given, the link to results will be sent to user.
    • A sample input can be seen by clicking the sample button given in the web server page.
    • When the processing is completed, you are automatically redirected to the results page, where the parameters you have supplied can be seen on top as:

 


Please cite: Kaya, C., Armutlulu, A., Ekesan, S., & Haliloglu, T. (2013). MCPath: Monte
Carlo path generation approach to predict likely allosteric pathways and
functional residues. Nucleic acids research, 41(W1), W249-W255.


For questions and comments: "mcpath AT prc.boun.edu.tr"