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Protein contact map prediction using multi-stage hybrid intelligence inference systems
Anas A Abu-Doleh1, Omar M Al-Jarrah, Asem Alkhateeb
1Department of Computer Engineering, Faculty of Computer and Information Technology, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan. a.abudoleh@yahoo.com
Journal of Biomedical Informatics
|November 15, 2011
Summary
This study introduces JUSTcon, a novel protein contact map predictor using adaptive neuro-fuzzy inference systems and K nearest neighbors. JUSTcon improves prediction accuracy, especially for long-range contacts, aiding protein 3D structure reconstruction.
Area of Science:
- Computational biology
- Structural bioinformatics
- Machine learning in bioinformatics
Background:
- Proteins are crucial biomolecules, and their 3D structure dictates function.
- Experimental structure determination lags behind sequence discovery, creating a need for accurate prediction methods.
- Protein contact map prediction is vital for reconstructing 3D protein structures.
Purpose of the Study:
- To develop a highly accurate protein contact map predictor.
- To address the persistent challenge of achieving precise contact map predictions.
- To improve the reconstruction of protein 3D structures.
Main Methods:
- Development of JUSTcon, a novel predictor employing parallel stages.
- Integration of adaptive neuro-fuzzy inference System (ANFIS) and K nearest neighbors (KNNs) classifier.
- Implementation of a smart filtering operation with an expert system for filter window size selection.
Main Results:
- Achieved an average accuracy of 45.2% for sequence separations of six amino acids.
- Demonstrated superior performance over SVMcon and PROFcon, particularly for large separation distances.
- Attained an average accuracy of 15% for sequence separations of 24 amino acids on CASP9 targets.
Conclusions:
- JUSTcon offers a significant advancement in protein contact map prediction accuracy.
- The predictor's effectiveness in handling long-range contacts aids in more reliable 3D structure modeling.
- JUSTcon contributes to bridging the gap between protein sequence and structure determination.
