ATRIPPI: An atom-residue preference scoring function for protein-protein interactions

Kang Ping Liu; Lu Shian Chang; Jinn-Moon Yang

doi:10.1109/BIBE.2009.45

ATRIPPI: An atom-residue preference scoring function for protein-protein interactions

Kang Ping Liu, Lu Shian Chang, Jinn-Moon Yang^*

^*Corresponding author for this work

Department of Biological Science and Technology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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 cocrystallized 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.

Original language	English
Title of host publication	Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009
Pages	392-399
Number of pages	8
DOIs	https://doi.org/10.1109/BIBE.2009.45
State	Published - 2009
Event	2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009 - Taichung, Taiwan Duration: 22 Jun 2009 → 24 Jun 2009

Publication series

Name	Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009

Conference

Conference	2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009
Country/Territory	Taiwan
City	Taichung
Period	22/06/09 → 24/06/09

Keywords

Atom-atom interacting preference
Knowledge-based scoring matrix
Protein-protein interaction
Residue-residue interaction preference

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10.1109/BIBE.2009.45

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Liu, K. P., Chang, L. S., & Yang, J.-M. (2009). ATRIPPI: An atom-residue preference scoring function for protein-protein interactions. In Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009 (pp. 392-399). Article 5211233 (Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009). https://doi.org/10.1109/BIBE.2009.45

Liu, Kang Ping ; Chang, Lu Shian ; Yang, Jinn-Moon. / ATRIPPI : An atom-residue preference scoring function for protein-protein interactions. Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009. 2009. pp. 392-399 (Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009).

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title = "ATRIPPI: An atom-residue preference scoring function for protein-protein interactions",

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 cocrystallized 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.",

keywords = "Atom-atom interacting preference, Knowledge-based scoring matrix, Protein-protein interaction, Residue-residue interaction preference",

author = "Liu, {Kang Ping} and Chang, {Lu Shian} and Jinn-Moon Yang",

year = "2009",

doi = "10.1109/BIBE.2009.45",

language = "English",

isbn = "9780769536569",

series = "Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009",

pages = "392--399",

booktitle = "Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009",

note = "2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009 ; Conference date: 22-06-2009 Through 24-06-2009",

}

Liu, KP, Chang, LS & Yang, J-M 2009, ATRIPPI: An atom-residue preference scoring function for protein-protein interactions. in Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009., 5211233, Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009, pp. 392-399, 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009, Taichung, Taiwan, 22/06/09. https://doi.org/10.1109/BIBE.2009.45

ATRIPPI: An atom-residue preference scoring function for protein-protein interactions. / Liu, Kang Ping; Chang, Lu Shian; Yang, Jinn-Moon.
Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009. 2009. p. 392-399 5211233 (Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Liu, Kang Ping

AU - Chang, Lu Shian

AU - Yang, Jinn-Moon

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N2 - 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 cocrystallized 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.

AB - 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 cocrystallized 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.

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KW - Knowledge-based scoring matrix

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KW - Residue-residue interaction preference

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Liu KP, Chang LS, Yang JM. ATRIPPI: An atom-residue preference scoring function for protein-protein interactions. In Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009. 2009. p. 392-399. 5211233. (Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009). doi: 10.1109/BIBE.2009.45

ATRIPPI: An atom-residue preference scoring function for protein-protein interactions

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