Model Evaluation, Refinement & Validation Training | Ramachandran, MolProbity, Map Fit, Phenix, Rosetta

Evaluate and refine protein models with best practices: geometry checks, Ramachandran, rotamers, clashscore, map fit, RMSD/QA metrics, and reproducible validation reports using Phenix, MolProbity, Coot, Rosetta, and PDB-REDO.

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Model Evaluation, Refinement & Validation — Hands-on

Turn draft structures into reliable models. Learn systematic evaluation of geometry and stereochemistry, density fit and map correlation, targeted refinement, and final validation bundles suitable for peer review and deposition.

Model Evaluation, Refinement & Validation (Ramachandran, RMSD, etc.)

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Session Index

Session 1 — Geometry & Stereochemistry Checks Session 2 — Map Fit & Density Validation Session 3 — Refinement Strategies Session 4 — Mini Capstone: Validate → Refine → Report

Session 1

Fee: Rs 6300

Geometry & Stereochemistry Checks

Fundamentals of model quality and common pathologies

Theory

Backbone and side chain diagnostics

Ramachandran rotamer outliers bond lengths/angles clashscore CaBLAM

Global and local QA metrics

RMSD/RMSF Verify3D ProSA/ERRAT WHAT_CHECK

Session 2

Fee: Rs 8400

Map Fit & Density Validation

X-ray and cryo EM validation concepts and metrics

Rwork/Rfree map model CC FSC

Cryo EM focused checks and tools

EMRinger Q score local resolution

Practical map inspection and model building fixes

Coot ChimeraX ISOLDE

Session 3

Fee: Rs 11200

Refinement Strategies

Real space and reciprocal space refinement workflows

Phenix refine/real space refine REFMAC5 overview PDB REDO concepts

Energy guided fixes and side chain repacking

Rosetta Relax/FastRelax SCWRL minimization basics

Water, ligands and alternate conformations

validation of occupancy and B factors chemistry checks

Session 4

Fee: Rs 14000

Mini Capstone: Validate → Refine → Report

Diagnose a model, apply targeted fixes, and re validate

Theory + Practical

Assemble depositor ready validation bundle

MolProbity summary map model metrics figures and tables

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums