Structural Bioinformatics Basics

Understand how dna replication, transcription, and translation drive the central dogma of molecular biology, linking dna as the life blueprint to rna and protein production in cells.

Explore how proteins act as the functioning machinery of cells, from ribosome synthesis to folding and degradation by the proteosome, and distinguish globular soluble proteins from structural non-soluble proteins.

Determine protein structures via X-ray crystallography, NMR spectroscopy, and electron microscopy to visualize function and mechanism; apply molecular dynamics, docking, and homology modeling for ligand insights and unknown structures.

nuclear magnetic resonance spectroscopy determines protein structures in aqueous solution by estimating proton distances with distance geometry methods, yielding an ensemble of models rather than a single structure.

Learn how amino acids with a central c-alpha carbon, carboxyl and amino groups form peptide bonds. These bonds create the primary structure by dehydration synthesis.

Explore backbone geometry of peptides, focusing on phi and psi rotations around the N–Cα and Cα–C bonds, with omega fixed, guided by Ramachandran principles of planarity, sterics, and hydrogen bonding.

Explore the hierarchy of protein structures from primary sequences of amino acids and peptide bonds to secondary motifs like helices, sheets, and loops, then to tertiary folds and quaternary assemblies.

Discover how protein motifs or super-secondary structures group secondary elements, including beta-alpha-beta, beta-hairpin, and alpha-alpha motifs, and how their polarity-driven side-chain distribution shapes globular protein domains.

Learn how protein structure stabilizes via covalent and non-covalent interactions, with hydrogen bonding sustaining alpha helices and beta sheets, and salt bridges, electrostatic, and van der waals forces.

Proteins fold into a unique, function-designating shape after synthesis on the ribosome, a process called the protein folding problem, with competing theories yet to reach a consensus.

Protein folding begins in the cytosol, where secondary structural elements interact with the solvent, entropy loss drives folding from disorderly state toward a molten globule state and defined tertiary structure.

Explore how protein function arises from subtle three-dimensional structures, with myoglobin storing oxygen and hemoglobin transporting oxygen, illustrating the link between structure and function in proteins.

Explore the Protein Data Bank, an international repository that freely provides 3D structural data for proteins and nucleic acids, determined by X-ray crystallography, NMR, or electron microscopy.

Learn the PDB file format, a standard textual representation of macromolecular structures with atomic coordinates, annotations for helices and sheets, residues, ligands, and mmcif alternatives.

Explore the SCOP database and its manually curated protein structure classification by class, fold, super-family, and family, including seven major classes and the concept of domains.

Explore CATH, a manually curated structural database that classifies proteins using class, architecture, topology, and homologous super-family based on secondary structure content.

Visualize molecules by rotating, translating, and zooming to inspect atoms, bonds, hydrogen bonds, and measure distances in space. Compare wire-frame and space-filling models of lysozyme, showing surface-charge density.

Visualize the lysozyme protein through ball-and-stick, backbone, ribbon, and surface models, colored by atom type, electrostatic potential, hydrophobicity, and solvent accessibility to reveal active-site pockets and charged residues.

Compare protein structures using global and local alignments and structural superposition, assess similarity with root mean square deviation, and apply alignment to classify structures and evaluate predicted models against templates.

Predict protein structures from known homologues using protein homology modeling, a structural bioinformatics technique that links structure to function and complements experimental methods like X-ray crystallography, NMR, and electron microscopy.

Identify a template by searching the Protein Data Bank, align target and template sequences, model with MODELLER, and evaluate the final structure for biological relevance.

Explore protein molecular dynamics by simulating motion with newtonian equations, using initial coordinates from x-ray crystallography, nmr, or electron microscopy, and evolving trajectories to reveal equilibrium behavior in biophysical environments.

Protein molecular docking is a bioinformatics technique in structure-based drug design, where known target and ligand structures are examined for binding, with binding energy calculations evaluating interaction strength.