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Structural Bioinformatics Basics
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Electron Microscopy
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.
Ramachandran Plot
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.
Structural Alignment
A form of sequence alignment based on comparing the three-dimensional structures of proteins. Used for identifying structural similarities and evolutionary relationships.
Sequence Alignment
A method of arranging the sequences of DNA, RNA, or protein to identify regions of similarity. Important in identifying functional, structural, or evolutionary relationships.
Beta Sheet
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.
Protein Folding
The process by which a protein structure assumes its functional shape or conformation. Applications include understanding diseases related to protein misfolding.
PDB (Protein Data Bank)
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.
NMR Spectroscopy
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.
Structural Motif
A particular combination of secondary structures that are present in many proteins. Used to classify proteins and predict function based on structure.
Docking
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.
Molecular Dynamics Simulation
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.
Homology Modeling
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.
Secondary Structure Prediction
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.
Alpha Helix
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.
X-ray Crystallography
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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