Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.
BACKGROUND
Elucidation of the full network of protein-protein interactions is crucial for understanding of the principles of biological systems and processes. Thus, there is a need for in silico methods for predicting interactions. We present a novel algorithm for automated prediction of protein-protein interactions that employs a unique bottom-up approach combining structure and sequence conservation in protein interfaces.


RESULTS
Running the algorithm on a template dataset of 67 interfaces and a sequentially non-redundant dataset of 6170 protein structures, 62 616 potential interactions are predicted. These interactions are compared with the ones in two publicly available interaction databases (Database of Interacting Proteins and Biomolecular Interaction Network Database) and also the Protein Data Bank. A significant number of predictions are verified in these databases. The unverified ones may correspond to (1) interactions that are not covered in these databases but known in literature, (2) unknown interactions that actually occur in nature and (3) interactions that do not occur naturally but may possibly be realized synthetically in laboratory conditions. Some unverified interactions, supported significantly with studies found in the literature, are discussed.


BACKGROUND
http://gordion.hpc.eng.ku.edu.tr/prism


BACKGROUND
agursoy@ku.edu.tr; okeskin@ku.edu.tr.
Aytuna
A Selim
AS
Koc University, Center for Computational Biology and Bioinformatics, College of Engineering, Rumelifeneri Yolu 34450 Sariyer, Istanbul, Turkey.
Gursoy
Attila
A
Keskin
Ozlem
O
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D017124:Conserved Sequence; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship
D011506:Proteins