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Structure- and sequence-based prediction of DNA-binding sites in DNA-binding proteins can be performed on several web servers listed below. DISIS predicts DNA binding sites directly from the amino acid sequence and hence is applicable for all known proteins. It is based on the chemical-physical properties of the residue and its environment ...
SMID-BLAST is a tool developed to annotate known small-molecule binding sites as well as to predict binding sites in proteins whose crystal structures have not yet been determined. The prediction is based on extrapolation of known interactions, found in the PDB, to interactions between an uncrystallized protein with a small molecule of interest.
Computational methods to identify the DNA binding sequence specificity have been proposed to make a good use of the abundant sequence data in the post-genomic era. [24] In addition, progress has happened on structure-based prediction of binding specificity across protein families using deep learning. [25]
DNA footprinting is a method of investigating the sequence specificity of DNA-binding proteins in vitro. This technique can be used to study protein-DNA interactions both outside and within cells. The regulation of transcription has been studied extensively, and yet there is still much that is unknown.
A unified interface for: Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues Automated webserver and some downloadable programs RaptorX: remote homology detection, protein 3D modeling, binding site prediction
Protein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex ...
DNA binding sites are regions in the genome sequence that bind to and interact with specific proteins. They play an important role in DNA replication and repair, transcriptional regulation, and viral infection. Binding site prediction involves the use of one of the following two methods: [49] Sequence similarity based methods. They consist in ...
ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest. Previously, ChIP-on-chip was the most common technique utilized to study these protein–DNA relations.