The document discusses the validation of homology modeling, emphasizing the importance of checking consistency with stereochemical standards and experimental data. It outlines various web tools and databases available for assessing the reliability of structural models, including detailed descriptions of specific tools like ERRAT, MolProbity, and Procheck. The validation process involves multiple aspects, including verifying measurements, consistency with experiments, and adherence to known physical and chemical properties.

1. Validation of
homology modeling
PRESENTED BY:
ALICHY SOWMYA
18PIM2855
M.S. (PHARM) 2ND SEM
NIPER, S.A.S NAGAR

2. • Validation is the process of checking that your model is consistent with
stereochemical standards i.e., validation is the process of evaluating
reliability
• The validation has three aspects:
1) Checking on the validity of the thousands to millions of
measurements in the experiment,
2) checking how consistent the atomic model is with those
experimental data and
3) checking consistency of the model with known physical and
chemical properties
Validation:

3. • There are a number of web tools and databases that may help in
assessing the reliability of structural models (crystallographic, NMR, or
homology based models)
Validation:

4. Databases:
EDS Electron Density Server - a collection of reports on
models from the PDB (for which experimental
crystallographic data has been deposited) with a focus
on the fit of the model to the data
PDBREPORT Database of automatically made WHAT CHECK reports
for all PDB entries
PDBsum Each entry Includes links to PROCHECK, WHAT
CHECK and EDS reports

5. Servers:
ERRAT Uses to analyze the statistics of non-bonded
interactions between different atom types.
Eval123D Performs the quality checks provided by the
programs Verify3D, Eval23D ProSA and EvTree.
JCSG Structure
Validation
Central
Performs any or all of the quality checks provided by
the
programs PROCHECK, SFCHECK, PROVE, ERRAT, WAS
P, DDQ, WHAT CHECK and PSQS.
MetaMQAPII Metaserver for quality assessment of protein
structures optimized for theoretical models
MolProbity Includes steric and geometric analyses.
PARVATI Analysis tool for macromolecular structure
refinements that include anisotropic displacement
parameters.
pdb-care Carbohydrate residue checks.
ProSA Fold reliability analysis.

6. Servers:
PSVS Performs the quality checks provided by the
programs PROCHECK, Verify3D, MolProbity ProSA an
d more.
Ramachandran
plot
Ramachandran plot analysis.
RAMPAGE Ramachandran plot analysis.
STAN the STructure ANalysis server, performs the quality
checks provided by the
programs WASP, CISPEP and MOLEMAN2
VADAR Volume, Area, Dihedral Angle Reporter. Includes
excluded volume, accessible surface area, backbone
and side chain dihedral angles, secondary structure,
hydrogen bonding partners, hydrogen bond energies,
steric quality, solvation free energy as well as local
and overall fold quality.
Verify3D Assessment of protein models with 3-D sequence
profiles.

7. Programs incorporated in the servers:
CISPEP Uses to investigate if any non-
proline peptide bond that has
been modeled as trans could in
reality be cis.
DDQ Difference density quality analysis.
MOLEMAN2 Includes geometry and dihedrals
angles analyses.
PROCHECK Includes stereochemical quality
checks.
PROVE Atomic volume check.
SFCHECK A program for assessing the
agreement between the atomic
model and X-ray data or EM map.

8. WASP Uses to investigate if certain water
molecules could be metal ions
instead.
WHAT CHECK A protein verification tools from
the WHAT-IF program. Includes
stereochemical, steric,
nomenclature, and packing quality
checks. The checks can be
accessed via WHAT-IF
servers (Build/check/repair model
server)
Programs incorporated in the servers:

9. Thank You!