Module 4: The Bioinformatician's Toolkit

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