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The GrAfSS (Graph theoretical Applications for Substructure searching) suite of programs allows users to search biological macromolecular structure data for specific 3D arrangements or motifs. This website is free and open to all users and there is no login requirement.

Citation for referencing GrAfSS:
Nur Syatila Ab Ghani, Reeki Emrizal, Sabrina Mohamed Moffit, Hazrina Yusof Hamdani, Effirul Ikhwan Ramlan, Mohd Firdaus-Raih, GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA, Nucleic Acids Research, 2022;, gkac402, https://doi.org/10.1093/nar/gkac402 HTML, PDF.

The 3D structure search functions covered by the GrAfSS server are:

  • searching a Protein or RNA structure for known 3D arrangements/motifs/sites;

  • searching available protein structures for presence of a specific 3D arrangement;

  • searching for specific clusters of hydrogen bonded RNA base interactions.


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    Begin your GrAfSS search:


     

    Search for the presence of 3D sites and motifs in a query protein structure. The output is a list of potential functional sites.

    Input / Query file PDB/mmCIF formatted protein structure file.
    Database options searched Known amino acid side chain arrangements and 3D motifs from various sources.
    OutputA list of potential 3D patterns found in the query protein structure

    Notes: 
    1. Please ensure that the query is a PDB/mmCIF formatted file.
    2. Submitted searches may take a few minutes to complete, please leave your browser on the page until the results are returned or use the link provided to retrieve the results. The program typically takes 1-5 minutes to complete depending on the size of your protein and the current server load. Thank you for your patience.

    Submit a Search

    Upload a PDB/mmCIF file:

    Or enter a 4-letter PDB ID: e.g., "4cha" or "4CHA"

    Include 2-residue patterns? (Compulsory) No Yes
    NOTE: Excluding 2-residue patterns is recommended.


    Do a demonstration run

    Click 'Submit' to do a demonstration SPRITE run:
    [Download sample input (Alpha-chymotrypsin - 4cha.pdb)]  [Submit]
    [Download sample input (Burkholderia Lethal Factor 1 (BLF1) - 3tu8.pdb)]  [Submit]
    [Download sample input (Hypothetical protein AF_1782 - 2oo2.pdb)]  [Submit]

     

     
     

    Search for the occurrences of specific 3D patterns of amino acid side chains in other protein structures (PDB formatted query structures).

    Input / Query file A specific 3D arrangement of amino acid residues in PDB format (not exceeding 12 residues).
    Database options searched Subsets of the PDB and selected AlphaFold2 proteomes (source: EBI).
    OutputA list of 3D protein structures containing the query pattern.

    Notes: 
    1. Your query should be a 3D amino acid pattern which will be used to search for other similar amino acid arrangements in a database of PDB structures.
    2. Please ensure that the query is a PDB formatted file.
    3. The query file cannot contain more than 12 amino acid residues.
    4. An error will be returned for queries exceeding 12 residues including cases where 12 or less residues have multiple positions (ie. from NMR).
    5. Queries submitted may take a few minutes to complete, please leave your browser on the page until the results are returned or use the link to retrieve the results (an ASSAM search typically runs for 1-5 minutes depending on the server load).


    Submit a Search

    Upload a PDB-formatted pattern:

    Database to compare against:


    Do a demonstration run

    Click 'Submit' to do a demonstration ASSAM run:
    [Download sample input (2atqRERE.pdb)]  [Submit]

     

     
     

    Search for whether hypothetical amino acid 3D arrangement can be found in available PDB structures. A users can design their own motif with specific residue types and distances between residues, with a flexible distance tolerance.


    Input / Query file A theoretical 3D arrangement of amino acid residues defined by distances between the residues (menu based selection and wild-card capability).
    Database options searched Subsets of the PDB and selected AlphaFold2 proteomes (source: EBI).
    Output A list of protein structures and respective 3D patterns containing the residue arrangement.

    To run a search:
    1. Select the number of residues for the query pattern from the list below (3-8 residues).
    2. Enter the specific residue or general type and set the distances between the residues.

    Notes for setting up your search:
    ALL residues must be connected as a whole, although not all distances need to be defined.
    For distances that are not defined, a wildcard value is used during the search.
    The distances entered will carry a variable tolerance value of (+/-)1.5 Angstroms.
    Please see example searches for assistance.

    Search times and output visualization:
    1. Each search may take time to complete depending on the complexity of the query and the server load. Users are advised to bookmark the results page or copy the link to the results for analysis at a later point in time.
    2. In order to use the output visualization features via Jmol, your web browser will need to be able to run Java. Please take note that there are known issues for Java 7 on the Chrome web browser for the Mac OSX operating system.
    3. Search results will be kept for at least 2 days. The main search results can be downloaded to your local computer while still retaining the server side ability to view the hits in Jmol.

    Demonstration run:
    Click 'Submit' to do a demonstration IMAAAGINE run:
    Search for a "Ser-[D/E]-Ser-[D/E]-Ser-[D/E]" arrangement [Submit]

     
     

    Search for amino acid 3D arrangements in a query protein that are similar to approved drug binding sites . Users may upload/ search a PDB structure.


    Input / Query file PDB/mmCIF file or PDB ID.
    Database searched Precomputed database of sites that have a similar amino acid 3D arrangement to that of known drug binding sites.
    OutputA list of potential 3D patterns similar to known drug binding sites found in the query protein structure

    Notes: 
    1. Please ensure that the query is a PDB/mmCIF formatted file.
    2. Submitted searches may take a few minutes to complete, pease leave your browser on the page until the results are returned or use the link provided to retrieve the results. The program typically takes 1-5 minutes to complete depending on the size of your protein and the current server load. Thank you for your patience.

    Residue arrangements in query structure similar to a known drug binding site

    Searching a protein structure for potential 3D drug binding patterns

    Upload a PDB/mmCIF file:

    Or enter a 4-letter PDB ID: e.g., "5eid" or "5EID"


     
     

    Search for 3D motifs and patterns of base arrangements in RNA (and RNA associated) PDB formatted query structures.

    Input / Query file PDB formatted RNA structure file.
    Database searched RNA base arrangements and 3D motifs.
    Output A list of potential 3D motifs in query RNA structure.

    Guide to submitting a search:
    1. Please ensure that the query structure is a PDB formatted file. (See test/demo submission)
    2. The program typically takes 2-5 minutes to complete depending on the size of your nucleic acid structure. Thank you for your patience.
    3. The distance tolerance has been set to an optimized value as the default.
       - To increase retrieval or coverage of the search, increase the distance tolerance value.
       (Note: This may also result in an increase of false positive results)

    Demonstration run:
    Click 'Submit' to do a demonstration NASSAM run:
    [Download sample input (6tna.pdb)]  [Submit]

     
     

    Searches for clusters of hydrogen bonded base interactions in RNA 3D structures.

    Input / Query file PDB formatted RNA structure file.
    Database searched High resolution subsets of RNA structures from the PDB.
    Output Hydrogen bonded base connections in query RNA structure.

    To run a search:
     STEP 1. Select to search either the option of (1) searching for a specific set of hydrogen bonded base connections in a database of RNA structures (sourced from the PDB) or (2) to upload an RNA structure (in PDB format) to annotate the hydrogen bonded base interactions present in the query structure.
    STEP 2. Select the number of residues and the arrangement of the interactions for the query patterns from the list provided (2-6 bases or select "All patterns" for arrangement types).
    STEP 3. For specific patterns selected in STEP 2; enter the specific residue or general type (for all base possibilities).
    For searches using Option 3; the difference is mainly in the requirement to have two structures uploaded. Please note that the program does not filter out highly dissimilar structures which are not useful comparisons.

    Search times and output visualization:
    1. Each search may take time to complete depending on the complexity of the query and the server load (usually completed within 2 minutes). Users are advised to bookmark the results page or copy the link to the results for analysis at a later point in time if a search takes more than 10 minutes.
    2. Please note that COGNAC output can be visualized using ngl.
    3. Search results will be kept for at least 2 days. The main search results can be downloaded to your local computer while still retaining the server side ability to view the hits in ngl.

    Demonstration run:
    Click 'Submit' to do a demonstration COGNAC run:
    [Download sample input (6tna.pdb)]  [Submit]



     

    Estimated run times: GrAfSS runs typically take 2-5 minutes to complete during light server loads. Very large inputs such as complex molecular assemblies have been tested to take 5-7 hours. The processing time during heavy server loads are expected to be longer.

    The GrAfSS server and the associated computer programs are developed and maintained by MFRLab.org at Universiti Kebangsaan Malaysia.

    The GrAfSS service is mirrored at:

  • Malaysia Genome and Vaccine Institute

  • ISPC, Weizmann Institute of Science (in progress)

  • Advanced Medical and Institute, Universiti Sains Malaysia (in progress)


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    Please bookmark or use http://mfrlab.org/grafss and not any IP address displayed in the browser.
    For enquiries or to report errors, please email info@mfrlab.org.