Validation of homology modeling
- 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!