Docking (molecular)In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction.
Polygon meshIn 3D computer graphics and solid modeling, a polygon mesh is a collection of , s and s that defines the shape of a polyhedral object. The faces usually consist of triangles (triangle mesh), quadrilaterals (quads), or other simple convex polygons (n-gons), since this simplifies rendering, but may also be more generally composed of concave polygons, or even polygons with holes. The study of polygon meshes is a large sub-field of computer graphics (specifically 3D computer graphics) and geometric modeling.
Deep learningDeep learning is part of a broader family of machine learning methods, which is based on artificial neural networks with representation learning. The adjective "deep" in deep learning refers to the use of multiple layers in the network. Methods used can be either supervised, semi-supervised or unsupervised.
Active siteIn biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the binding site, and residues that catalyse a reaction of that substrate, the catalytic site. Although the active site occupies only ~10–20% of the volume of an enzyme, it is the most important part as it directly catalyzes the chemical reaction.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
Geometry processingGeometry processing, or mesh processing, is an area of research that uses concepts from applied mathematics, computer science and engineering to design efficient algorithms for the acquisition, reconstruction, analysis, manipulation, simulation and transmission of complex 3D models. As the name implies, many of the concepts, data structures, and algorithms are directly analogous to signal processing and .
Protein designProtein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch (de novo design) or by making calculated variants of a known protein structure and its sequence (termed protein redesign). Rational protein design approaches make protein-sequence predictions that will fold to specific structures.
Polygonal modelingIn 3D computer graphics, polygonal modeling is an approach for modeling objects by representing or approximating their surfaces using polygon meshes. Polygonal modeling is well suited to scanline rendering and is therefore the method of choice for real-time computer graphics. Alternate methods of representing 3D objects include NURBS surfaces, subdivision surfaces, and equation-based (implicit surface) representations used in ray tracers. The basic object used in mesh modeling is a vertex, a point in three-dimensional space.
Solid modelingSolid modeling (or solid modelling) is a consistent set of principles for mathematical and computer modeling of three-dimensional shapes (solids). Solid modeling is distinguished within the broader related areas of geometric modeling and computer graphics, such as 3D modeling, by its emphasis on physical fidelity. Together, the principles of geometric and solid modeling form the foundation of 3D-computer-aided design and in general support the creation, exchange, visualization, animation, interrogation, and annotation of digital models of physical objects.
Drug designDrug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient. In the most basic sense, drug design involves the design of molecules that are complementary in shape and charge to the biomolecular target with which they interact and therefore will bind to it.
