Basics of Computational Structure Biology (Protein)

Conceptual Basics

1. Amino Acids , Their Properties , and Their Main Functions in Lives
2. Dihedral Angles and Ramachandran plot
3. Secondary Structure Propensity: Alpha-Helix

Comparison of helix propensity in proteins

Alpha-helix propensity within the context of a folded protein

The distribution of alpha-helix propensity along the polypeptide chain is not conserved

Helix propensity of Ala and Val

Alpha helix propensity of amino acids

Structural basis of amino acid alpha helix propensity

Beta-Sheet:

Context is a major determinant of beta-sheet propensity.

Heterogeneity of packing: structural approach

Protein thermal stability: hydrogen bonds or internal packing?

Effect of packing density on chain conformation

Hydrogen bonding, hydrophobicity, packing, and protein folding

An analysis of packing in the protein folding problem

A survey of atom packing in globular proteins.

Does packing determine the native fold?

Determinants of protein side-chain packing

Does optimal sidechain packing determine the native sequence?

6. Hydrophobicity
7. Conformational Change
8. Protein Folding Problem
9. Inverse Protein Folding Problem
10. Protein-Ligand Interaction
11. Random Coil: A Reference State

---

Theoretical Framework