Quest D, Ali H: The Motif Tool Assessment Platform (MTAP) for sequence-based transcription factor binding site prediction tools. Methods Mol Biol 2010, 674:121-41.Quest D, Ali H: The Motif Tool Assessment Platform (MTAP) for sequence-based transcription factor binding site prediction tools....
We have evaluated a set of transcription factor binding site prediction tools that could be downloaded and installed locally, identifying FIMO and MCAST as the best-performing tools for identifying individual TFBSs and clusters of TFBSs respectively. While it is possible that there is some inter-re...
Benchmarking TFBS prediction webtools TFBS predictions on various human genes were performed using TFBSPred and other webtools, mostly using the default settings. Gene names were submitted to TFBSPred. FASTA-formatted gene regulatory sequences were submitted to AliBaba2.1(45), TFBIND (46), SITECON...
STarMir Tools for Prediction of microRNA Binding Sites Authors: Shaveta Kanoria 1 , William Rennie 1 , Chaochun Liu 1 , C. Steven Carmack 1 ... Ye Ding 1 Shaveta Kanoria 1 , William Rennie 1 , Chaochun Liu 1 , C. Steven Carmack 1 , Jun Lu 2 , Ye Ding 1 ...
Using protein binding site prediction to improve protein docking - ScienceDirect Predicting protein interaction interfaces and protein complexes are two important related problems. For interface prediction, there are a number of tools, ... B Huang,M Schroeder - 《Gene》 被引量: 145发表: 2008年 CA...
Multiple other machine learning-based protein–protein interaction site prediction methods have been developed7,35,36,37. We introduce here PeSTo, a parameter-free geometric transformer that acts directly on the atoms of a protein structure. As shown in Fig. 1 and detailed in Methods, the ...
We have developed a novel graph-theoretic algorithm, MotifClick, forcis-regulatory binding site prediction, and have demonstrated that it outperforms several current leading motif-finding tools on both synthetic and real datasets, especially when the nucleotide distribution of a motif is similar to th...
Predicting the functional sites of a protein from its structure, such as the binding sites of small molecules, other proteins or antibodies, sheds light on its function in vivo. Currently, two classes of methods prevail: machine learning models built on
However, scientists still routinely use TF binding site (TFBS) search tools to scan unannotated sequences for TFBSs, particularly when searching for lesser-known TFs or TFs in organisms for which ChIP-seq data are unavailable. The sequence analysis often involves multiple steps such as TF model ...
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