A Method For Discriminating Native Protein-DNA Complexes From Decoys Using Spatial Specific Scoring Matrices
Decoding protein-DNA interactions is important to understanding gene regulation and has been investigated by worldwide scientists for a long time.However,many aspects of the interactions still need to be uncovered.The crystal structures of protein-DNA complexes reveal detailed atomic interactions between the proteins and DNA and are an excellent resource for investigating the interactions.In this study,we profiled the spatial distribution of protein atoms around six structural components of the DNA,which are the four bases,the deoxyribose sugar and the phosphate group.The resultant profiles not only revealed the preferred atomic interactions across the protein-DNA interface but also captured the spatial orientation of the interactions.The profiles are a useful tool for investigating protein-DNA interactions.We tested the strength of profiles in two experiments,discrimination of native protein- DNA complexes from decoys with mutant DNA and discrimination of native protein-DNA complexes from nearnative docking decoys.The profiles achieved an average Z-score of 7.41 and 3.22 respective on benchmark datasets for the tests,both are better than other knowledge-based energy functions that model protein-DNA interaction based on atom pairs.
protein-DNA interaction spatial specific scoring matrix fragment-based method
Wen Cheng Changhui Yan
Department of Computer ScienceNorth Dakota State University Fargo, ND, USA
国际会议
7th International Conference on Systems Biology(第7届计算系统生物学国际研讨会)(ISB2013)
安徽黄山
英文
115-118
2013-08-22（万方平台首次上网日期，不代表论文的发表时间）