text: Protein science, from an amino acid to sequences and structures
  Proteins are large, complex molecules that playing critical roles to maintain the normal functioning of the human body. They are essential not just for the structure and function, but also the regulation among the body's tissues and organs. Proteins are made up of hundreds of smaller units called amino acids that are attached to one another by peptide bonds, forming a long chain.
  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 comparison. Most of the algorithms for active site detection are based on geometric modeling or energetic features based calculation.
  The role of protein pockets
  The shape and properties of the protein surface determine what interactions are possible with ligands and other macromolecules. Pockets are an important yet ambiguous feature of this surface. During drug discovery process, the first step in screening for lead compounds and potential molecules as drugs is usually a selection of the shape of the binding pocket. Shape plays a role in many computational pharmacological methods. Based on existing results, most features important to predicting drug-binding were depended on size and shape of the binding pocket, with the chemical properties of secondary importance. The surface shape is also important for interactions between protein and water. However, defining discrete pockets or possible interaction sites still remains unclear, due to the shape and location of nearby pockets affected promiscuity and diversity of binding sites. Since most pockets are open to solvent, to define the border of a pocket is the primary difficulty. Those closed to solvent we refer to as buried cavities. With the benefit of well-defined extent, area and volume, buried cavities are more straightforward to locate. In contrast, the border of an open pocket defines its mouth and it provides the cut-off for determination of the surface area and volume. Even defining the pocket as a set of residues does not define the volume or the mouth of the pocket.
  Druggability role prediction
  In pharmaceutical industry, the current priority strategy for target assessment is high-throughput screening (HTS). NMR screenings are applied against large compound datasets. Chemical characteristics of compounds binding against specific targets are measured, so how well the compound sets bind to the chemical space will decide the binding efficiency. Success rates of virtually docking of the drug-like ligands into the active sites of the target proteins would be detected for prioritization, while the most of the active sites located at the pockets.
  With the benefits of large amount of structural data, computational methods from different perspectives for druggability prediction have been introduced during the last 30 years with positive results, as a vital instrument to accelerate the prediction accessibility.  Many candidates have been integrated into drug discovery pipeline already since then.