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.
The 3D structure search functions covered by the GrAfSS server are:
Estimated run times: 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 associated computer programs are developed and maintained by MFRLab.org at Universiti Kebangsaan Malaysia.
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
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. |
| Output | A list of potential 3D patterns found in the query protein structure. |
Search for the occurrences of specific 3D patterns of amino acid side chains in other protein structures (PDB formatted query structures).
| Input / Query file | PDB/mmCIF formatted protein structure 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). |
| Output | A list of 3D protein structures containing the query pattern. |
Click Submit to do a demonstration ASSAM run:
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. |
Click Submit to do a demonstration IMAAAGINE run:
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 options searched | Precomputed database of sites that have a similar amino acid 3D arrangement to that of known drug binding sites. |
| Output | A list of potential 3D patterns similar to known drug binding sites found in the query protein structure. |
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 options searched | RNA base arrangements and 3D motifs. |
| Output | A list of potential 3D motifs in query RNA structure. |
Searches for clusters of hydrogen bonded base interactions in RNA 3D structures.
| Input / Query file | PDB formatted RNA structure file. |
|---|---|
| Database options searched | High resolution subsets of RNA structures from the PDB. |
| Output | Hydrogen bonded base connections in query RNA structure. |