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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 ...
In immunology, epitope mapping is the process of experimentally identifying the binding site, or epitope, of an antibody on its target antigen (usually, on a protein). [1] [2] [3] Identification and characterization of antibody binding sites aid in the discovery and development of new therapeutics, vaccines, and diagnostics.
Recent advances in chromatin immunoprecipitation followed by sequencing have provided powerful ways to identify genome-wide profiling of DNA-binding proteins and histone modifications. [1] [2] The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.
Binding of a ligand to a binding site on protein often triggers a change in conformation in the protein and results in altered cellular function. Hence binding site on protein are critical parts of signal transduction pathways. [10] Types of ligands include neurotransmitters, toxins, neuropeptides, and steroid hormones. [11]
This list of protein subcellular localisation prediction tools includes software, databases, and web services that are used for protein subcellular localization prediction. Some tools are included that are commonly used to infer location through predicted structural properties, such as signal peptide or transmembrane helices , and these tools ...
Protein active sites. Usually, the active site of a protein locates on its center of action and, the key to its function. The first step is the detection of active sites on the protein surface and an exact description of their features and boundaries. These specifications are vital inputs for subsequent target druggability prediction or target ...
ProBiS is a computer software which allows prediction of binding sites and their corresponding ligands for a given protein structure. Initially ProBiS was developed as a ProBiS algorithm by Janez Konc and Dušanka Janežič in 2010 [1] and is now available as ProBiS server, ProBiS CHARMMing server, ProBiS algorithm and ProBiS plugin.
Binding site prediction involves the use of one of the following two methods: [49] Sequence similarity based methods. They consist in the identification of homologous sequences with known DNA binding sites, or by aligning them with query proteins. Their performance is usually low because the DNA binding sequences are less conserved.