This document discusses protein structure, classification, prediction, and visualization. It covers secondary structure elements like alpha helices and beta sheets, as well as tertiary and quaternary structure. It describes protein structure databases like the Protein Data Bank and tools for visualizing protein structures. Different amino acid properties that influence secondary structure are also discussed.

1. Protein
Classification
And Structure
prediction

2. Ramachandran plot

3. Turns and Loops

4. Tertiary structure
Motifs:
-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

5. Stable folding patterns in proteins

6. Stable folding patterns in proteins

7. Stable folding patterns in proteins

8. Stable folding patterns in proteins

9. Quaternary structure
The spatial arrangement of different subunits
Forces involved are,
1. Vander Waals
2. London Dispersions
3. Salt bridges
4. H-bonds

10. Protein structure classification
1. Alpha or α/α
2. Beta or β /β
3. Alpha/Beta or α/β
4. Alpha and Beta or α+β

11. Steric properties of amino acids can greatly affect the local
structures that a protein adopts
Structural configuration Amino acid
Propensity for alpha-helix Ala, Leu, Glu
Disrupt alpha-helix Ser, Asp, Asn
Propensity for Beta-sheets and
disrupt alpha-helix Val and Ile
Propensity for turns Gly, Pro, Asp

12. Protein structure Databases
Protein Data Bank
Large 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 their
visualization and comparative analysis

13. Protein structure Visualization
Databases and tools
Cn3-D
Structure and sequence alignment viewer for NCBI databases
RasMol
One of the most popular tools for protein structure visualization
Swiss-PDB Viewer
An interface to analyze several proteins at the same time
It is tightly linked to Swiss-model, an automated homology
modelling server

14. Protein structure Visualization
Databases and tools
Kinemage
An illustration presented as an interactive computer display
PDBsum
Pictorial summary of the key information on each
macromolecular structure from PDB

15. Protein structure alignment
VAST (Vector alignment Search Tool)
Developed at NCBI
Used to identify similar protein 3D structures in MMDB/PDB
DALI Server
An automated protein structure alignment tool

16. Domain Architecture Databases
CDD (Conserved Domain Database)
NCBI database
Collection of sequence alignments and profiles, representing
protein