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Protein ClassificationAnd Structureprediction
Ramachandran plot
Turns and Loops
Tertiary structureMotifs: -Also called supersecondary structures or folds-Stable arrangements of several elements of secondary structure and connections between them
Domains: Polypeptides with more than a few hundred amino acid residues often fold into two or more stable, globular units
Stable folding patterns in proteins
Stable folding patterns in proteins
Stable folding patterns in proteins
Stable folding patterns in proteins
Quaternary structureThe spatial arrangement of different subunits
Forces involved are,1. Vander Waals2. London Dispersions3. Salt bridges4. H-bonds
Protein structure classification1. Alpha or α/α 2. Beta or β /β3. Alpha/Beta or α/β 4. Alpha and Beta or α+β
Steric properties of amino acids can greatly affect the localstructures that a protein adopts
Structural configuration Amino acidPropensity for alpha-helix Ala, Leu, GluDisrupt alpha-helix Ser, Asp, AsnPropensity for Beta-sheets and disrupt alpha-helix Val and IlePropensity for turns Gly, Pro, Asp
Protein structure DatabasesProtein Data BankLarge global repository for the processing and distribution of 3-D macromolecular structure data (experimental)
MMDB (Molecular modelling Database)Macromolecular 3D structures as well as tools for theirvisualization and comparative analysis
Protein structure Visualization Databases and tools
Cn3-DStructure and sequence alignment viewer for NCBI databases
RasMolOne of the most popular tools for protein structure visualization
Swiss-PDB Viewer An interface to analyze several proteins at the same timeIt is tightly linked to Swiss-model, an automated homologymodelling server
Protein structure Visualization Databases and tools
KinemageAn illustration presented as an interactive computer display
PDBsumPictorial summary of the key information on each macromolecular structure from PDB
Protein structure alignment
VAST (Vector alignment Search Tool)Developed at NCBIUsed to identify similar protein 3D structures in MMDB/PDB
DALI ServerAn automated protein structure alignment tool
Domain Architecture Databases
CDD (Conserved Domain Database)NCBI databaseCollection of sequence alignments and profiles, representing protein