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Coot displays electron density maps and atomic models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, and Ramachandran idealization. The software is designed to be easy-to-learn for novice users, achieved by ensuring that ...
A protein contact map represents the distance between all possible amino acid residue pairs of a three-dimensional protein structure using a binary two-dimensional matrix. For two residues i {\displaystyle i} and j {\displaystyle j} , the i j {\displaystyle ij} element of the matrix is 1 if the two residues are closer than a predetermined ...
There are several families that function in amino acid transport, some of these include: TC# 2.A.3 - Amino Acid-Polyamine-Organocation (APC) Superfamily; TC# 2.A.18 - Amino Acid/Auxin Permease (AAAP) Family; TC# 2.A.23 - Dicarboxylate/Amino Acid:Cation (Na + or H +) Symporter (DAACS) Family; TC# 2.A.26 - Branched Chain Amino Acid:Cation ...
A good example of composite models is the Nicholson approach, widely used from the late 1970s for building models of biological macromolecules. The components are primarily amino acids and nucleic acids with preformed residues representing groups of atoms. Many of these atoms are directly moulded into the template, and fit together by pushing ...
By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. [1] To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions , such as hydrogen bonding , ionic interactions , Van der Waals forces , and ...
The primary structure of a biopolymer is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry).For a typical unbranched, un-crosslinked biopolymer (such as a molecule of a typical intracellular protein, or of DNA or RNA), the primary structure is equivalent to specifying the sequence of its monomeric subunits, such as amino ...
An electron transport chain (ETC [1]) is a series of protein complexes and other molecules which transfer electrons from electron donors to electron acceptors via redox reactions (both reduction and oxidation occurring simultaneously) and couples this electron transfer with the transfer of protons (H + ions) across a membrane.
Structure of a typical L-alpha-amino acid in the "neutral" form. Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. [1] Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. [2]