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Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Protein–protein complexes are the most commonly attempted targets of such modelling, followed by protein–nucleic acid complexes. The ultimate goal of docking is the prediction of the three-dimensional structure of the macromolecular complex of interest as it would occur in a living organism. Docking itself only produces plausible candidate structures. These candidates must be ranked using methods such as scoring functions to identify structures that are most likely to occur in nature. The term "docking" originated in the late 1970s, with a more restricted meaning; then, "docking" meant refining a model of a complex structure by optimizing the separation between the interactors but keeping their relative orientations fixed. Later, the relative orientations of the interacting partners in the modelling was allowed to vary, but the internal geometry of each of the partners was held fixed. This type of modelling is sometimes referred to as "rigid docking". With further increases in computational power, it became possible to model changes in internal geometry of the interacting partners that may occur when a complex is formed. This type of modelling is referred to as "flexible docking". == Background == The biological roles of most proteins, as characterized by which other macromolecules they interact with, are known at best incompletely. Even those proteins that participate in a well-studied biological process (e.g., the Krebs cycle) may have unexpected interaction partners or functions which are unrelated to that process. In cases of known protein–protein interactions, other questions arise. Genetic diseases (e.g., cystic fibrosis) are known to be caused by misfolded or mutated proteins, and there is a desire to understand what, if any, anomalous protein–protein interactions a given mutation can cause. In the distant future, proteins may be designed to perform biological functions, and a determination of the potential interactions of such proteins will be essential. For any given set of proteins, the following questions may be of interest, from the point of view of technology or natural history: * Do these proteins bind ''in vivo''? If they do bind, * What is the spatial configuration which they adopt in their bound state? * How strong or weak is their interaction? If they do not bind, * Can they be made to bind by inducing a mutation? Protein–protein docking is ultimately envisaged to address all these issues. Furthermore, since docking methods can be based on purely physical principles, even proteins of unknown function (or which have been studied relatively little) may be docked. The only prerequisite is that their molecular structure has been either determined experimentally, or can be estimated by a protein structure prediction technique. Protein–nucleic acid interactions feature prominently in the living cell. Transcription factors, which regulate gene expression, and polymerases, which catalyse replication, are composed of proteins, and the genetic material they interact with is composed of nucleic acids. Modeling protein–nucleic acid complexes presents some unique challenges, as described below. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Macromolecular docking」の詳細全文を読む スポンサード リンク
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