# Module 4: The Bioinformatician's Toolkit

> Navigate the PDB, sequence alignment, conservation analysis and structure prediction.

Sequences, structures, and the tools to explore them

Navigate the PDB, sequence alignment, conservation analysis and structure prediction.

- Read a PDB file and extract the metadata that qualifies the coordinates: method, resolution, chains and ligands
- Navigate a 3D viewer and colour a structure by the property that answers your question
- Interpret BLAST output and read a multiple sequence alignment for conserved and variable positions
- Map conservation onto a structure to locate functional sites that sequence alone cannot pinpoint
- Interpret pLDDT and PAE, and tell a confident prediction from a confidently wrong one
- Compare the current prediction methods and choose between them for a given problem

## Links

- [Introduction](https://proteindesign.academy/module/4/intro)
- [4.1 Reading a PDB File](https://proteindesign.academy/module/4/1)
- [4.2 Navigating a 3D Molecular Viewer](https://proteindesign.academy/module/4/2)
- [4.3 Sequence Alignments and BLAST](https://proteindesign.academy/module/4/3)
- [4.4 Evolutionary Conservation and ConSurf](https://proteindesign.academy/module/4/4)
- [4.5 Structure Prediction Landscape](https://proteindesign.academy/module/4/5)
- [The Structural Biologist](https://proteindesign.academy/module/4/capstone)
- [Use the Tools](https://proteindesign.academy/module/4/tools)
- [Start Here](https://proteindesign.academy/start-here)
- [Tools & Papers](https://proteindesign.academy/tools-and-papers)
- [Continuing Practice](https://proteindesign.academy/continuing-practice)