NDLI: ATRIPPI: An Atom-residue Preference Scoring Function for Protein-protein Interactions

Content Provider	IEEE Xplore Digital Library
Author	Kang-Ping Liu Lu-Shian Chang Jinn-Moon Yang
Copyright Year	2009
Abstract	We present an ATRIPPI model for analyzing protein-protein interactions. This model is a 167-atom-type and residue-specific interaction preferences with distance bins derived from 641 co-crystallized protein-protein interfaces. The ATRIPPI model is able to yield physical meanings of hydrogen bonding, disulfide bonding, electrostatic interactions, van der Waals and aromatic-aromatic interactions. We applied this model to identify the native states and near-native complex structures on 17 bound and 17 unbound complexes from thousands of decoy structures. On average, 77.5% structures (155 structures) of top rank 200 structures are closed to the native structure. These results suggest that the ATRIPPI model is able to keep the advantages of both atom-atom and residue-residue interactions and is a potential knowledge-based scoring function for protein-protein docking methods. We believe that our model is robust and provides biological meanings to support protein-protein interactions.
Starting Page	392
Ending Page	399
File Size	1496805
Page Count	8
File Format	PDF
ISBN	9780769536569
DOI	10.1109/BIBE.2009.45
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-06-22
Publisher Place	Taiwan
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Protein engineering Biological system modeling Atomic measurements Bioinformatics Hydrogen Electrostatics Bonding Large-scale systems Biomedical engineering Biology residue-residue interaction preference protein-protein interaction atom-atom interacting preference knowledge-based scoring matrix
Content Type	Text
Resource Type	Article

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