A Selim Aytuna | PubMed Health

PubMed2005

PRISM: protein interactions by structural matching.

Prism (http://gordion.hpc.eng.ku.edu.tr/prism) is a website for protein interface analysis and prediction of putative protein-protein interactions. It is composed of a database holding protein interface structures derived from the Protein Data Bank (PDB). The server also includes summary information about related proteins and an interactive protein interface viewer. A list of putative protein-protein interactions obtained by running our prediction algorithm can also be accessed. These results are applied to a set of protein structures obtained from the PDB at the time of algorithm execution (January 2004). Users can browse through the non-redundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of similar structures to these interfaces or see the results of interaction predictions for a particular protein. Another service provided is interactive prediction. This is done by running the algorithm for user input structures.

Algorithms↗

PubMed2005

Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.

MOTIVATION: 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. AVAILABILITY: http://gordion.hpc.eng.ku.edu.tr/prism CONTACT: agursoy@ku.edu.tr; okeskin@ku.edu.tr.

Algorithms↗