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