2月12日,生物学领域重要期刊Briefings in Bioinformatics在线发表了我校人工智能学院计智伟教授课题组题为“ULDNA: Integrating Unsupervised Multi-Source Language Models with LSTM-Attention Network for High-Accuracy Protein-DNA Binding Si...
MetaDBSite integrates the prediction results from six available online web servers: DISIS, DNABindR, BindN, BindN-rf, DP-Bind and DBS-PRED and it only uses sequence information of proteins. A large dataset of DNA-binding proteins are constructed from the Protein Data Bank and serves as a ...
wedetailthemeta-analysisofproteinDNA-bindingsites.Wealsoproposespecificimplicationsthatarelikelytoresultinnovelpredictionmethods,increasedperformance,orpracticalapplications.Keywords:DNA-bindingsite;prediction;machinelearningmethod;bioinformaticsOPENACCESSInt.J.Mol.Sci.2015,1651951.IntroductionProtein–DNAinteractionsare...
Comparison of DNA-binding site prediction methods.Mu, GaoJeffrey, Skolnick
several bioinformatics methods have also been developed for the prediction of DNA binding site complementing experimental procedures. The computational approaches for prediction of DNA binding site and DNA-binding proteins can be broadly classified into three categories: sequenced based approaches, structure-...
GMean—a semi-supervised GRU and K-mean model for predicting the TF binding site Chai Wen Chuah Wanxian He De-Shuang Huang Scientific Reports(2024) Selective gene expression maintains human tRNA anticodon pools during differentiation Lexi Gao ...
However, bioinformatical searches relying only on the DNA motif (the nucleotide sequence of the binding site) for predicting a TFBS besides predicting the correct binding site often produce false positive results (overprediction), for example due to not considering TF-TF protein interactions in the...
v1.0). The software was modified in such a way that would allow to incorporate merging of the output into non-intersecting genome regions by means of bedtools and then assessing the predictive power of the model given these regions. The support vector machine prediction was performed using R-...
Table 2 Binding free energies and equilibrium dissociation constant of Dbh and the mutants to primer/template DNA. Full size table Experimental determination of the equilibrium dissociation constant (Kd) To validate the computational prediction of the binding affinity of Dbh and the variants to template...
The sequencing and analysis of 11.8 Mb from the centromere-flanking region ofhuman chromosome16p and 16q was reported by Loftuset al.[1•]. This region was revealed to be gene poor, with only 84 predicted genes. Genes identified only by gene prediction software were not included in this ...