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| Graph
theoretic methods for the analysis of structural relationships in
biological macromolecules |
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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. PDF
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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
Primary References:
1.
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.
2. 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:
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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
Primary References:
1.
Firdaus-Raih et al.: Novel base triples in RNA
structures revealed by graph theoretical searching methods. BMC
Bioinformatics 2011 12(Suppl 13):S2.
2. 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. |
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The
SPRITE (3D Search for PRotein sITEs) 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
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Computational resources provided by the Genome Computing Centre, Malaysia Genome Institute
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