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UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. [1]
The 3D structure of the protein AP5M1. The alpha fold structure was obtained from Uniprot (AF-Q9H0R1-F1) and modeled using ChimeraX. The three domains are emphasized with color. The first domain is yellow, the second domain is teal, and the third domain is pink.
Zoomed in ZIP7 3D Alpha Fold structure modeled in ChimeraX. No zinc atom is present. The dark blue helix is TM4 and the orange helix is TM5. The red residues are amino acids involved in binding to two zinc atoms. [10] Accession number: AF-Q92504-F1 [13] There are no experimentally solved structures of ZIP7 in its entirety. [13]
Secondary Structure Matching (SSM) — a tool for protein structure comparison. Uses RMSD. GDT, LCS and LGA — different structure comparison measures. Description and services. SuperPose — a protein superposition server. Uses RMSD. superpose — structural alignment based on secondary structure matching. By the CCP4 project.
Interpretation of PAE values allows scientists to understand the level of confidence in the predicted structure of a protein: Lower PAE values between residue pairs from different domains indicate that the model predicts well-defined relative positions and orientations for those domains.
The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with single letter codes. The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined ...
The brilliant iridescent colors of the peacock's tail feathers are created by structural coloration, as first noted by Isaac Newton and Robert Hooke.. Structural coloration in animals, and a few plants, is the production of colour by microscopically structured surfaces fine enough to interfere with visible light instead of pigments, although some structural coloration occurs in combination ...
Ten years after James Watson and Francis Crick published their model of the DNA double helix, [2] Karst Hoogsteen reported [3] a crystal structure of a complex in which analogues of A and T formed a base pair that had a different geometry from that described by Watson and Crick. Similarly, an alternative base-pairing geometry can occur for G ...