Structural Alignment with Dali

Overview

Teaching: 30 min
Exercises: 90 min

Questions

• How are similar protein structures identified?

Objectives

• Students will distinguish between sequence and structure alignments and also between local and global alignments.

• Students will interpret Dali output (specifically: Z-score, RMSD, and sequence identity) to identify structurally similar proteins.

• Students will infer functional information about a query/unknown protein based on a hit/known protein.

Dali is a structural alignment tool that aligns entire protein structures. The quality of the match is indicated by the z-score. Other information that can be determined from a Dali search includes the RMSD between the query structure and the similar protein, the length of the alignment, and the sequence similarity between the proteins.

Module Resources

Download student module here

Key Points

• Dali searches identify backbone structure similarity between a query protein and 3D structures of proteins from the PDB.

• Backbone structure similarity may not guarantee similarity in function since side chains are important for function.