ERAS AfricaLearning
Course catalogue · Computational drug discovery

Molecular Docking using Python

From a public structure to a docked pose and a defensible analysis, worked end to end on five real HIV drug targets.

Online, self paced2.3 hours5 modules · 20 lessons3.5 CEUNarratedCertificate
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What you will learn

  • Define target, ligand, binding pocket, pose and docking score and use each word correctly.
  • Explain what structure based drug design does and where docking sits inside it.
  • Install and verify a working Python environment for cheminformatics and structural work.
  • Build molecules from SMILES with RDKit and compute the descriptors that matter for drug likeness.
  • Prepare a receptor and a ligand correctly, including hydrogens, protonation and rotatable bonds.
  • Define a search box that contains the pocket without wasting search effort.
  • Implement a grid based pocket volume measurement and explain every step of it.
  • Handle structures that contain several copies of the same ligand correctly.
  • Structure an analysis notebook so that a stranger can rerun it end to end.
  • Record data provenance for every external source used.

Syllabus

5 modules, each with a knowledge check
🧬1. Foundations of structure based drug discoveryTarget, ligand, pocket, pose and score. Five words that carry the whole pipeline, learned on real HIV structures.4 lessons · 27 min
  1. 1.1 Five words7 min
  2. 1.2 What makes a molecule a medicine7 min
  3. 1.3 Five targets on one virus7 min
  4. 1.4 The question this course answers6 min

Objectives. Define target, ligand, binding pocket, pose and docking score and use each word correctly. Explain what structure based drug design does and where docking sits inside it. State the drug likeness properties that decide whether a molecule can be a tablet. Name the five drug targets used through this course and the step of the HIV life cycle each one serves. Explain why lenacapavir is the question this whole course is built around.

🐍2. The Python toolkit and real dataOne environment, seven packages, two public databases, and every number fetched rather than typed.4 lessons · 28 min
  1. 2.1 A working environment7 min
  2. 2.2 Molecules in Python with RDKit7 min
  3. 2.3 Fetching chemistry from PubChem7 min
  4. 2.4 Structures from the Protein Data Bank7 min

Objectives. Install and verify a working Python environment for cheminformatics and structural work. Build molecules from SMILES with RDKit and compute the descriptors that matter for drug likeness. Query PubChem programmatically for molecular weight, lipophilicity and structure, with caching and retries. Download experimental structures from the Protein Data Bank and read their atom and ligand records. Record provenance so that every number in your analysis can be traced to a public source.

⚙️3. Preparing and running a dockClean the files, place the box, run the search, read the poses, then prove the method works by redocking.4 lessons · 28 min
  1. 3.1 Preparing the files7 min
  2. 3.2 The box and the search7 min
  3. 3.3 Running Vina and reading the output7 min
  4. 3.4 Redocking and what it proves7 min

Objectives. Prepare a receptor and a ligand correctly, including hydrogens, protonation and rotatable bonds. Define a search box that contains the pocket without wasting search effort. Set and justify exhaustiveness, number of modes and the random seed. Run AutoDock Vina from Python and read the pose table without over reading the score. Validate a docking protocol by redocking a known ligand and computing the root mean square deviation.

📐4. Measuring pockets and analysingCount the empty space around a real ligand, check it against an independent tool, then test the association four ways.4 lessons · 27 min
  1. 4.1 Measuring the empty space7 min
  2. 4.2 Copies, and the error that was caught7 min
  3. 4.3 Cross validation and the statistics7 min
  4. 4.4 Reading the result honestly6 min

Objectives. Implement a grid based pocket volume measurement and explain every step of it. Handle structures that contain several copies of the same ligand correctly. Cross validate a measurement against an independently built tool and report the disagreement. Test an association with correlation, regression, bootstrap confidence intervals, a randomisation null and leave one out analysis. Describe how a real error was found in this project and how it was disclosed.

📓5. Reproducibility, reporting and your studyA notebook a stranger can rerun, a methods section a reviewer can check, and a protocol for your own question.4 lessons · 28 min
  1. 5.1 A notebook anybody can rerun7 min
  2. 5.2 Writing it for review7 min
  3. 5.3 Limits and responsible use7 min
  4. 5.4 Capstone, your own study protocol7 min

Objectives. Structure an analysis notebook so that a stranger can rerun it end to end. Record data provenance for every external source used. Write a methods and results section that a reviewer can verify without contacting you. State the limits of a docking and structural analysis, including what must never be claimed. Write a protocol for your own docking study with its validation step planned in advance.

Pre-test 15 items before Module 1, not graded  ·  Post-test 30 items, pass mark 80%  ·  Capstone a written plan you export and keep

How it is taught

Narrated micro lessons

Every screen has recorded narration that adds context and examples from Ethiopian hospitals. Lessons are five to ten minutes and resume where you stopped, on any device.

Decisions, not slides

Branching scenarios, matching, ordering and short written tasks with immediate feedback and the reasoning, whichever way you answer.

Blended option

Five ninety minute laboratory sessions, one per module, each ending with working code on the learner own machine.

Tools for Monday

Printable ward cards, checklists and audit forms are linked from the modules and free to adapt.

Frequently asked

How long do I have?

There is no deadline. Most learners finish in one to three weeks of short sessions. Your progress is saved to your account.

Is there a cost?

No. Enrolment, the course, the certificate and the resources are free.

What if I fail the post-test?

You can retake it. The feedback after each item tells you which module to revisit.

Is the certificate recognised for licence renewal?

The certificate states the CEU value calculated at one CEU per hour of learning in line with the national CPD Guideline, with a verification number. Recognition for licence renewal depends on accreditation by the CPD accreditor, which ERAS Africa and the EAA are pursuing.

Can my hospital run it as a workshop?

Yes. Each module has a facilitated 90 minute session plan. Contact ERAS Africa through the website to arrange a cohort.