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Molecular Viewer - 3D Visualization of Molecules and Crystal Structures
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Protein Visualization Controls
About Protein Structures
Proteins are complex macromolecules made up of chains of amino acids. They fold into specific three-dimensional structures that are essential for their biological function.
Structural Hierarchy
Primary structure: The sequence of amino acids.
Secondary structure: Regular patterns like alpha helices and beta sheets.
Tertiary structure: The overall 3D structure of a single protein chain.
Quaternary structure: The arrangement of multiple protein chains in a complex.
Common Visualization Methods
Cartoon/Ribbon: Shows secondary structure elements.
Ball & Stick: Shows atomic bonds clearly.
Space-filling: Shows the volume occupied by atoms.
Surface: Shows the molecular surface and binding pockets.
Important Features
Active sites: Where enzymatic reactions occur.
Binding sites: Where ligands, substrates, or other proteins bind.
Disulfide bonds: Covalent bonds that stabilize protein structure.
Domains: Functional or structural units within proteins.
Coloring Schemes
By chain: Different colors for different protein chains.
By secondary structure: Different colors for helices, sheets, and loops.
By residue type: Colors based on amino acid properties.
By B-factor: Indicates flexibility or uncertainty in structure.