Related Experiment Video
Updated: Nov 28, 2025
A Modified Yeast-one Hybrid System for Heteromeric Protein Complex-DNA Interaction Studies
Published on: July 24, 2017
DBP-PSSM: Combination of Evolutionary Profiles with the XGBoost Algorithm to Improve the Identification of
Yanping Zhang1, Pengcheng Chen1, Ya Gao1
1School of Mathematics and Physics Science and Engineering, Hebei University of Engineering, Handan 056038,China.
Background And Objective:
DNA-binding proteins play important roles in a variety of biological processes, such as gene transcription and regulation, DNA replication and repair, DNA recombination and packaging, and the formation of chromatin and ribosomes. Therefore, it is urgent to develop a computational method to improve the recognition efficiency of DNA-binding proteins.
Methods:
We proposed a novel method, DBP-PSSM, which constructed the features from amino acid composition and evolutionary information of protein sequences. The maximum relevance, minimum redundancy (mRMR) was employed to select the optimal features for establishing the XGBoost classifier, therefore, the novel model of prediction DNA-binding proteins, DBP-PSSM, was established with 5-fold cross-validation on the training dataset.
Results:
DBP-PSSM achieved an accuracy of 81.18% and MCC of 0.657 in a test dataset, which outperformed the many existing methods. These results demonstrated that our method can effectively predict DNA-binding proteins.
Conclusion:
The data and source code are provided at https://github.com/784221489/DNA-binding.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
01:49Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
01:03Single-Strand DNA Binding Proteins