Protein Structure Prediction & Modeling — Hands-on

End-to-end structure prediction: pick good templates, align with care, model with the right engine, refine sensibly, and validate rigorously. Covers homology, threading, and ab initio/deep-learning hybrids with reproducible reporting.

Protein Structure Prediction & Modeling (Homology, Threading, Ab Initio)

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Session Index

Session 1 — Templates & Alignments Session 2 — Homology Modeling Session 3 — Threading & Ab Initio/DL Session 4 — Mini Capstone: Build→Refine→Validate

Session 1

Fee: Rs 6300

Templates & Alignments

Sequence prep, domain parsing & disorder/topology screens

UniProt Pfam TMHMM/SignalP IUPred

Template search and MSA construction

BLAST/PSI-BLAST HHsearch/HHblits MMseqs2 PDB/PDBe

Alignment curation & coverage checks for modeling readiness

gap handling secondary structure cues template quality

Session 2

Fee: Rs 8400

Homology Modeling

Model building with templates: loops & side-chains

MODELLER SWISS-MODEL RosettaCM

Model selection, restraint usage & basic minimization

DOPE/GA341 SCWRL/Side-chain packing stereo checks

Automating multi-template workflows & reports

Snakemake Conda/Mamba

Session 3

Fee: Rs 11200

Threading & Ab Initio / Deep Learning

Fold recognition & threading strategies

I-TASSER Phyre2 RaptorX

Ab initio & DL-guided pipelines and confidence metrics

AlphaFold RoseTTAFold ESMFold pLDDT/PAE

Topology checks, disordered regions & domain stitching

per-domain modeling linker handling

Session 4

Fee: Rs 14000

Mini Capstone: Build → Refine → Validate

From sequence to final model with provenance

Theory + Practical

Refinement: side-chains, loops, relaxation & energy minimization

Rosetta relax GROMACS minimization OpenMM

Validation bundle & deliverables

Ramachandran MolProbity ProSA/Verify3D PAE maps PDF/CSV + checksums

PDF

Protein Structure Prediction & Modeling Training | Homology, Threading, Ab Initio (MODELLER, I-TASSER, AlphaFold)

Protein Structure Prediction & Modeling — Hands-on