Capstone End-to-End Structural Modeling Project — Hands-on

Apply everything learned in structural bioinformatics, docking and molecular dynamics to a single coherent project. This capstone walks through scoping a realistic problem, selecting targets and inputs, planning workflows, running modeling and simple dynamics style analyses and packaging the results into a reproducible report and presentation suitable for academic or industry review.

Capstone End-to-End Structural Modeling Project

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Session Index

Session 1 — Scoping, Targets & Inputs Session 2 — Workflow & Modeling Plan Session 3 — Execution, Analysis & Checks Session 4 — Final Report, Slides & Repro Pack

Session 1

Fee: Rs 8800

Scoping, Targets & Inputs

Define a realistic structural modeling question

enzyme, receptor or complex of interest ligands, partners or mutations in scope success criteria and outputs expectation

Gather sequences, structures and experimental context

sequence variants and domain boundaries PDB or AlphaFold like models as starting points known ligands or assay conditions overview

Decide modeling depth vs time and compute budget

structure only vs docking plus dynamics style number of systems and replicates idea timeline and milestone sketch for project

Session 2

Fee: Rs 11800

Workflow & Modeling Plan

Design an end to end modeling workflow outline

structure curation and preparation steps docking and complex generation ideas MD style equilibration and production concepts

Choose key analyses and readouts in advance

RMSD, contacts and simple energy views binding site occupancy or pose stability variants or conditions comparison plan

Plan directory layout, naming and tracking for reproducibility

clear folders for inputs, runs and results simple metadata and log files concept script or notebook based automation ideas

Session 3

Fee: Rs 14800

Execution, Analysis & Checks

Run modeling, docking and basic dynamics style steps

prepared structures and complexes short MD like trajectories for stability views capture runs, parameters and seeds in notes

Perform core analyses and sanity checks on outputs

time series for RMSD and key distances interaction and contact pattern summaries simple convergence and quality checks

Compare conditions, ligands or variants against objectives

tables of metrics across systems short narrative on winners and losers flags for results needing caution

Session 4

Fee: Rs 18800

Final Report, Slides & Repro Pack

Draft a structured report telling the project story

Theory + Practical

Prepare figures, tables and slides for presentation

key structure and trajectory snapshots comparison charts across systems clear takeaway messages for each figure

Assemble the reproducible project pack for handover

notebooks or scripts with instructions input and config file checklist brief note on limits and future improvements

PDF

Capstone End-to-End Structural Modeling Project Training | From Scope to Reproducible Report

Capstone End-to-End Structural Modeling Project — Hands-on