We also show that many motif features composed by the residues which play important roles in DNA-protein interactions have large discriminant powers. It indicates that CNNsite has very good ability to extract important motif features for DNA-binding residue prediction....
Prediction of DNA-binding residues from sequence information using convolutional neural network Most DNA-binding residue prediction methods overlooked the motif features which are important for the recognition between protein and DNA. In order to effi... J Zhou,Q Lu,R Xu,... - 《Int.j.data Min...
Sequence-based approach for motif prediction is of great interest and remains a challenge. In this work, we develop a local combinational variable approach for sequence-based helix-turn-helix (HTH) motif prediction. First we choose a sequence data set for 88 proteins of 22 amino acids in lengt...
Pathway analyses for genes regulated by DNA methylation were performed using Ingenuity Pathway Analysis (QIAGEN) (https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/). The transcription factor (TF) binding motif prediction was performed us...
motif, it is the second of the two helices (counting from the N-terminal end) that is responsible forDNA binding. In the HLH motif, the two α-helices are responsible for dimerization of the protein, not DNA binding per se. Sometimes identical subunits form dimers; in other cases, the ...
However, most of these methods involve extensive manual feature engineering, which can be time-consuming and can require in-depth domain knowledge.Results: We propose a novel machine-learning method for poly(A) motif prediction by marrying generative learning (hidden Markov models) and discriminative...
Convolutional neural network architectures for predicting DNA–protein binding CNN用于基因组学研究的最大优势之一是,它可以探测某一motif(指蛋白质分子具有特定功能的或者作为一个独立结构域一部分相近的二级结构聚合体)是否在指定序列窗口内,这种探测能力非常有利于motif的鉴定,进而有助于结合位点的分类...
四、蛋白质-蛋白质相互作用界面(PPI):Binder设计核心知识点:RFdiffusion设计能有效介导蛋白间相互作用的Binder区域应用案例:1、ppi.hotspots:识别和利用PPI热点信息来定制Binder结构2、设计实例:针对指定骨架和/或特定motif的Binder结构创建 五、RFdiffusion中的对称性设计核心知识点:阐述如何在蛋白质结构设计中考虑并实现...
Predicting protein–DNA binding specificity is a challenging yet essential task for understanding gene regulation. Protein–DNA complexes usually exhibit binding to a selected DNA target site, whereas a protein binds, with varying degrees of binding spec
Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly underst