Protein-protein interaction affinity prediction based on interface descriptors and machine learning

Xue Ling Li, Min Zhu, Xiao Lai Li, Hong Qiang Wang, Shulin Wang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

Knowing the protein-protein interaction affinity is important for accurately inferring the time dimensionality of the dynamic protein-protein interaction networks from a viewpoint of systems biology. The accumulation of the determined protein complex structures with high resolution facilitates to realize this ambitious goal. Previous methods on protein-protein interaction affinity (PPIA) prediction have achieved great success. However, there is still a great space to improve prediction accuracy. Here, we develop a support vector regression method to infer highly heterogeneous protein-protein interaction affinities based on interface properties. This method takes full advantage of the labels of the interaction pairs and greatly reduces the dimensionality of the input features. Results show that the supervised machine leaning methods are effective with R=0.80 and SD=1.41 and perform well when applied to the prediction of highly heterogeneous or generic PPIA. Comparison of different types of interface properties shows that the global interface properties have a more stable performance while the smoothed PMF obtains the best prediction accuracy.

Original languageEnglish (US)
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages205-212
Number of pages8
Volume7390 LNAI
DOIs
StatePublished - 2012
Externally publishedYes
Event8th International Conference on Intelligent Computing Theories and Applications, ICIC 2012 - Huangshan, China
Duration: Jul 25 2012Jul 29 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7390 LNAI
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other8th International Conference on Intelligent Computing Theories and Applications, ICIC 2012
CountryChina
CityHuangshan
Period7/25/127/29/12

Fingerprint

Protein-protein Interaction
Descriptors
Affine transformation
Learning systems
Machine Learning
Proteins
Prediction
Dimensionality
Support Vector Regression
Protein Interaction Networks
Protein Structure
Systems Biology
Complex Structure
High Resolution
Interaction
Labels

Keywords

  • Machine Learning
  • Potential of Mean Force
  • protein complex interface descriptors
  • Protein-protein interaction affinity
  • two-layer Support Vectors

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Li, X. L., Zhu, M., Li, X. L., Wang, H. Q., & Wang, S. (2012). Protein-protein interaction affinity prediction based on interface descriptors and machine learning. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 7390 LNAI, pp. 205-212). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7390 LNAI). https://doi.org/10.1007/978-3-642-31576-3_27

Protein-protein interaction affinity prediction based on interface descriptors and machine learning. / Li, Xue Ling; Zhu, Min; Li, Xiao Lai; Wang, Hong Qiang; Wang, Shulin.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7390 LNAI 2012. p. 205-212 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7390 LNAI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Li, XL, Zhu, M, Li, XL, Wang, HQ & Wang, S 2012, Protein-protein interaction affinity prediction based on interface descriptors and machine learning. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 7390 LNAI, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7390 LNAI, pp. 205-212, 8th International Conference on Intelligent Computing Theories and Applications, ICIC 2012, Huangshan, China, 7/25/12. https://doi.org/10.1007/978-3-642-31576-3_27
Li XL, Zhu M, Li XL, Wang HQ, Wang S. Protein-protein interaction affinity prediction based on interface descriptors and machine learning. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7390 LNAI. 2012. p. 205-212. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-31576-3_27
Li, Xue Ling ; Zhu, Min ; Li, Xiao Lai ; Wang, Hong Qiang ; Wang, Shulin. / Protein-protein interaction affinity prediction based on interface descriptors and machine learning. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7390 LNAI 2012. pp. 205-212 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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