Graph theoretic methods for the analysis of structural relationships in biological macromolecules

Subgraph isomorphism and maximum common subgraph isomorphism algorithms from graph theory provide an effective and efficient way of identifying structural relationships between biological macromolecules. They thus provide a natural complement to the pattern matching algorithms that are used in bioinformatics to identify sequence relationships. Methods available here are applicable to different types of biological macromolecules from carbohydrates to protein and nucleic acid structures.

Reference:
Peter J. Artymiuk, Ruth V. Spriggs and Willett, P. (2005) Graph theoretic methods for the analysis of structural relationships in biological macromolecules. Journal of the American Society for Information Science and Technology, 56, 518-528.
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The ASSAM program searches for 3D patterns of amino acid side chains in PDB formatted query structures.

Go to ASSAM main page

Input / Query file:
Amino acid residues in PDB format (not exceeding 12 residues)
Database searched:
PDB and PDB subsets


Primary References:

1. Nadzirin et al.: SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures. Nucleic Acids Research. 2012 Jul;40(Web Server issue):W380-6. Epub 2012 May 9. HTML, PDF

2. Spriggs RV, Artymiuk PJ, Willett P. (2003) Searching for patterns of amino acids in 3D protein structures. J Chem Inf Comput Sci. Mar-Apr;43(2):412-21.

3. Artymiuk PJ, Poirrette AR, Grindley HM, Rice DW, Willett P. (1994) A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J Mol Biol. Oct 21;243(2):327-44.
Upload file to submit for ASSAM search:
 

The SPRITE server searches for protein sites and motifs in a query protein structure. The output is a list of potential functional sites.

Go to SPRITE main page

Input / Query file: PDB formatted protein structure file
Database searched:
Amino acid side chain arrangements and 3D motifs


Primary References:

1. Nurul Nadzirin, Eleanor Gardiner, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2012. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures. Nucleic Acids Research, Vol. 40, W380-W386doi: 10.1093/nar/gks401. HTML PDF

2. Spriggs RV, Artymiuk PJ, Willett P. (2003) Searching for patterns of amino acids in 3D protein structures. J Chem Inf Comput Sci. Mar-Apr;43(2):412-21.




Upload file to submit for SPRITE search:

 

The IMAAAGINE program allows users to search for hypothetical amino acid 3D arrangement query to be searched against the PDB. Users design their own motif with specific residue types and distances between residues, with a flexible distance tolerance.

Go to IMAAAGINE main page

Input / Query file:
Distanced based theoretical arrangement of amino acid residues (menu based selection and wild-card capability)
Database searched:
PDB and PDB subsets


Primary Reference:
1. Nurul Nadzirin, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2013. IMAAAGINE: a webserver for the searching of hypothetical 3D amino acid side chain arrangements in the Protein Data Bank. Nucleic Acids Research, Vol. 41: W432-W440. doi: 10.1093/nar/gkt431. (IF=8.278) HTML, PDF
 
The NASSAM program searches for 3D motifs and patterns of bases in RNA (and RNA associated) PDB formatted query structures.

Go to NASSAM main page


Input / Query file:
PDB formatted RNA structure file
Database searched:
RNA base arrangements and 3D motifs

Primary References
:
1.Hazrina Yusof Hamdani, Sri Devan Appasamy, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2012. NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules. Nucleic Acids Research, Vol. 40, W35-W41. doi: 10.1093/nar/gks513. HTML, PDF

2. Mohd Firdaus-Raih, Anne-Marie Harrison, Peter Willett, Peter J. Artymiuk. 2011. Novel base triples in RNA structures revealed by graph theoretical searching methods. BMC Bioinformatics, 12(S13), S2. doi:10.1186/1471-2105-12-S13-S2. 

3. Harrison, A-M, South, D.R., Willett, P., and Artymiuk, P.J. (2003) Representation, searching and discovery of patterns of bases in complex RNA structures. Journal of Computer-Aided Molecular Design, 17, 537-549.

Search RNA Structure for: (in PDB format)

All motifs/interactions except base pairs
Include computed hydrogen bonding interactions

 
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The COGNAC program that analyses and annotates hydrogen bonded interactions between bases in RNA 3D structures.

Input / Query file: PDB formatted RNA structure file

Go to COGNAC main page


Primary Reference:

Mohd Firdaus-Raih, Hazrina Yusof Hamdani, Nurul Nadzirin, Effirul Ikhwan Ramlan, Peter Willett, Peter J. Artymiuk. 2014. COGNAC: a webserver for searching and annotating hydrogen bonded base interactions in RNA 3-dimensional structures. Nucleic Acids Research, Vol. 42. doi: 10.1093/nar/gku438.
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