Interface-to-Interface
(I2I)-SiteEngine compares pairs of interacting protein binding sites.
Interface-to-Interface (I2I)-SiteEngine:a method for
structural alignment between two
protein-protein interfaces
Abstract:
Protein-protein interfaces, which are
regions of interaction between two protein molecules, contain the
information regarding patterns of
interacting functional groups.
I2I-SiteEngine simultaneously aligns between two pairs of binding sites
that constitute an
interface.
I2I-SiteEngine is based on recognition of similarity of
physico-chemical properties and shapes. Therefore it can
recognize similar interfaces shared by evolutionary unrelated proteins
with totally different sequences and folds.
Short Presentation: with graphical
explanations about the method and its applications.
Reference: Shulman-Peleg A., Mintz S., Nussinov
R, Wolfson HJ.Protein-Protein Interfaces: Recognition of
Similar Spatial and
Chemical
Organizations, In Jonassen and J. Kim (Eds.): Algorithms in
Bioinformatics: 4th International Workshop, WABI 2004, Bergen, Norway,
2004. Springer Verlag (2004), Lecture Notes in Computer Science, Volume
3240, pp. 194-205[PDF]
Contact:Alexandra
Shulman-Peleg shulmana@post.tau.ac.il
Application: Classification of
protein-protein interfaces for recognition of similar spatial and
chemical organizations
I2I-SiteEngine
was applied to classify apilot
dataset that contains some of the common protein-protein interfaces. As
a result, these 64 interfaces were clustered into 22 different groups. Some of the clusters
include
similar interfaces comprised by proteins with different structural
folds. This may suggest that certain interface binding
organizations may be shared by different protein families.
Furthermore, similar interfaces may suggest not only similar binding
organizations may also suggest similarity in binding partners and
function. Click
here to view the details of the obtained clusters. Click
here to view the default parameters used in this study.
