Measurement of protein surface shape by solid angles
Journal of Molecular Graphics
Approximate decision algorithms for point set congruence
Computational Geometry: Theory and Applications
On the approximation of largest common subtrees and largest common point sets
Theoretical Computer Science
MultiProt - A Multiple Protein Structural Alignment Algorithm
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Computing Largest Common Point Sets under Approximate Congruence
ESA '00 Proceedings of the 8th Annual European Symposium on Algorithms
Recognition of binding patterns common to a set of protein structures
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
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A protein-protein interface (PPI) is defined by a pair of regions of two interacting protein molecules that are linked by non-covalent bonds. Recognition of conserved 3D patterns of physico-chemical interactions may suggest their importance for the function as well as for the stability and formation of the protein-protein complex. It may assist in discovery of new drug leads that target these interactions. We present a novel method, MAPPIS, for multiple structural alignment of PPIs which allows recognition of a set of common physico-chemical properties and their interactions without the need to assume similarity of sequential patterns or backbone patterns. We show its application to several biological examples, such as alignment of interfaces of G proteins with their effectors and regulators, as well as previously created clusters of interfaces. Availability: The program and supplementary information, including colored figures, can be found at: http://bioinfo3d.cs.tau.ac.il/mappis/