Dali server: conservation mapping in 3D

TLDR

The Dali server provides web‑based protein structure comparison using the Dali program. Its purpose is to enable interactive analysis of residue conservation and ligand clustering across multiple structural alignments. The interface offers three modules—online Dali comparison, a browsable database of precomputed neighbourhoods, and a pairwise alignment tool—each with its own query form, accepting PDB IDs or uploads, and presenting hyperlinked results for interactive exploration. When successful, structure comparison can uncover evolutionary relationships that sequence analysis alone may miss.

Abstract

Our web site (http://ekhidna.biocenter.helsinki.fi/dali_server) runs the Dali program for protein structure comparison. The web site consists of three parts: (i) the Dali server compares newly solved structures against structures in the Protein Data Bank (PDB), (ii) the Dali database allows browsing precomputed structural neighbourhoods and (iii) the pairwise comparison generates suboptimal alignments for a pair of structures. Each part has its own query form and a common format for the results page. The inputs are either PDB identifiers or novel structures uploaded by the user. The results pages are hyperlinked to aid interactive analysis. The web interface is simple and easy to use. The key purpose of interactive analysis is to check whether conserved residues line up in multiple structural alignments and how conserved residues and ligands cluster together in multiple structure superimpositions. In favourable cases, protein structure comparison can lead to evolutionary discoveries not detected by sequence analysis.