We further analyzed the results for different carbohydrate-binding site classes. For monosaccharide- or disaccharide-binding site prediction, DeepGlycanSite showed outstanding performance with the average MCC and precision, more than twice those of the alternative methods (Fig.3a, b, dand Supplementary ...
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 ...
Motivation: An important step in structure-based drug design consists in the prediction of drug- gable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug compound, have been developed over the years by clever exploitation of geometric, chemical an...
BindN has been frequently accessed, and the prediction results have been shown to provide useful information for biological research [20]. Since our approach does not require structural information for binding site prediction, BindN+ can be used for genome-wide analyses of DNA and RNA-binding ...
Results We evaluated a set ofde novomotif discovery tools that could be downloaded and installed locally using ENCODE-ChIP-Seq data and showed that rGADEM was the best-performing tool. TFBS prediction tools used to scan PWMs against DNA fall into two classes — those that predict individual TF...
Tubiana, J., Schneidman-Duhovny, D. & Wolfson, H.J. ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction.Nat Methods19, 730–739 (2022). https://doi.org/10.1038/s41592-022-01490-7 ...
In this study, an effective SPR-based analysis strategy, including active ingredient screening, affinity determination, and binding site prediction, was established and used to identify and verify anti-inflammatory candidates of RPA. This strategy made full use of the technical advantages of SPR and ...
3DLigandSite utilizes protein-structure prediction to provide structural models for proteins that have not been solved. Ligands bound to structures similar to the query are superimposed onto the model and used to predict the binding site. In benchmarking against the CASP8 targets 3DLigandSite ...
Recently, deep learning based models have been proposed and have shown competitive results on a transcription factor binding site prediction task. However, it is difficult to interpret the prediction results obtained from the previous models. In addition, the previous models assumed all the sequence ...
Results Interferon beta 1 (IFNB1) enhanceosome To assess the predictive capabilities of TFBSPred and other TFBS prediction webtools, the IFNB1 enhanceosome (57) was used. The enhanceosome is an ~50 bp enhancer sequence of the IFNB1 gene and requires the coordinate activation and DNA bindin...