Structurally variable regions like loops, insertions and deletions can complicate protein structure modeling. The structure of an equivalent length segment from a homologous protein provides a guide for modeling missing regions, though the chosen segment may not always fit properly. De novo prediction involves using rotamer libraries of common amino acid conformations to predict side chain positions. Model validation checks the stereochemical accuracy, packing quality, and folding reliability of the predicted structure.

1. Structurally variable
regions

2. Loops, Insertions, Deletions complicate the process of
Modeling
A good guide for modeling the missing region can be
The structure of a segment of equivalent length in a
homologous protein
Loop search programs

3. Chosen segment may not fit properly into the existing
framework of the model
?
?
?
de novo prediction

4. o Identical residues or substituted residue pairs in homologous
proteins adopt similar conformations
If amino acids to be substituted are not related
Solution:
Rotamer libraries
Ex: Ponder and Richards library (67 rotamers of 17 amino
acids)
(Rotamers are conformers that differ by rotation about only a
sigma bond. i.e., only one dihedral angle will be different b/w
rotamers)
Side chain modeling

5. Offers the possibility to examine all the reference proteins
simultaneously to impose structural constraints
That in turn can be used to generate conformations consistent
with the data set
Distance geometry approach

6. Force fields used:
1. AMBER: United atom model and all-atom representations
can be applied
2. GROMOS: offers only united atom model
Molecular dynamics simulations:
United atom potential energy functions are used
SHAKE algorithm
Optimization

7. Model validation
Stereochemical accuracy
- Torsion angles
- Planarity of peptide bonds
- Chirality of C-alpha atoms
- Bond lengths
- Bond angles
Example: PROCHECK

8. Model validation

9. Model validation
Packing Quality
- Interatomic distances
- Secondary structural elements
- Hydrophobicity
- Solvent accessible surface of amino acids

10. Model validation
Folding reliability
- 3D-comparison model/template structure
- 3D-1D profiles
- Energy based comparison