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Protein–lipid interaction is the influence of membrane proteins on the lipid physical state or vice versa.. The questions which are relevant to understanding of the structure and function of the membrane are: 1) Do intrinsic membrane proteins bind tightly to lipids (see annular lipid shell), and what is the nature of the layer of lipids adjacent to the protein?
A benchmark of 84 protein–protein interactions with known complexed structures has been developed for testing docking methods. [15] The set is chosen to cover a wide range of interaction types, and to avoid repeated features, such as the profile of interactors' structural families according to the SCOP database.
A binding interaction between a small molecule ligand and an enzyme protein may result in activation or inhibition of the enzyme. If the protein is a receptor, ligand binding may result in agonism or antagonism. Docking is most commonly used in the field of drug design — most drugs are small organic molecules, and docking may be applied to:
This group of methods [11] [9] [12] [13] [14] makes use of known protein complex structures to predict and structurally model interactions between query protein sequences. The prediction process generally starts by employing a sequence based method (e.g. Interolog) to search for protein complex structures that are homologous to the query ...
Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction. Protein function is a broad term: the roles of proteins range from catalysis of biochemical reactions to transport to signal ...
In 2006, random forest, an example of a supervised technique, was found to be the most-effective machine learning method for protein interaction prediction. [57] Such methods have been applied for discovering protein interactions on human interactome, specifically the interactome of Membrane proteins [58] and the interactome of Schizophrenia ...
A protein structure prediction method must explore the space of possible protein structures which is astronomically large. These problems can be partially bypassed in "comparative" or homology modeling and fold recognition methods, in which the search space is pruned by the assumption that the protein in question adopts a structure that is ...
Path integral molecular dynamics (PIMD) is a method of incorporating quantum mechanics into molecular dynamics simulations using Feynman path integrals. In PIMD, one uses the Born–Oppenheimer approximation to separate the wavefunction into a nuclear part and an electronic part. The nuclei are treated quantum mechanically by mapping each ...