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Structural Bioinformatics Basics

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Electron Microscopy

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A technique using a beam of electrons to create an image of the specimen. Applications include visualizing the structure of large protein complexes and cellular components.

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Ramachandran Plot

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A plot of the torsion angles phi (φ) and psi (ψ) of amino acid residues in a protein structure. It is used to identify the possible conformations of peptides.

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Structural Alignment

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A form of sequence alignment based on comparing the three-dimensional structures of proteins. Used for identifying structural similarities and evolutionary relationships.

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Sequence Alignment

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A method of arranging the sequences of DNA, RNA, or protein to identify regions of similarity. Important in identifying functional, structural, or evolutionary relationships.

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Beta Sheet

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A secondary structure found in proteins consisting of beta strands connected laterally by at least two or three backbone hydrogen bonds. Applications include protein engineering and understanding protein structure-function relationships.

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Protein Folding

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The process by which a protein structure assumes its functional shape or conformation. Applications include understanding diseases related to protein misfolding.

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PDB (Protein Data Bank)

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A database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. Applications include research and education in biochemistry, and molecular biology.

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NMR Spectroscopy

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A physical phenomenon in which nuclei in a magnetic field absorb and re-emit electromagnetic radiation. Used in structural biology to determine the structure of proteins and nucleic acids in solution.

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Structural Motif

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A particular combination of secondary structures that are present in many proteins. Used to classify proteins and predict function based on structure.

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Docking

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Computational technique that predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Applications include rational drug design.

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Molecular Dynamics Simulation

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A computer simulation technique for studying the physical movements of atoms and molecules, and is used to analyze and predict the structure, dynamics, and thermodynamics of biological macromolecules.

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Homology Modeling

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A computational biology technique for constructing an atomic-resolution model of a protein from its amino acid sequence and an experimental structure of a homologous protein. Used in drug discovery and understanding protein function.

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Secondary Structure Prediction

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The process of predicting the local secondary structures of proteins and RNA based on their sequences. Helps in understanding the function and interaction of proteins and RNA.

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Alpha Helix

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A common secondary structure of proteins, characterized by a right-handed helix with a repeating pattern of hydrogen bonds. Applications include designing peptides and proteins with specific properties.

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X-ray Crystallography

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A technique used to determine the atomic and molecular structure of a crystal by diffracting X-ray beams through them. Applications include drug design and structural determination of biomolecules.

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