MSA-tools

Run conservation analysis on your protein structure(s) and visualise it in 3D

The use of the Rate4Site program is free for academic end-users & solely for non-commercial research purposes (Rate4Site Terms of use). Please do not use this tool if this is not the case.

Using Rate4Site, this tool will calculate evolutionary rates of the residues within your protein and map them onto your protein structure. You can upload a protein structure as .pdb or .cif file or enter a PDB code, as well as restrict the analysis to a given set of chains. MSA inputs are optional (they are generated with MMseqs2 if not given).

Example output: DHS-ERK2 complex (PDB: 8PVU); see Help pages for more information.

Protein structure

Upload a structure file (either .cif or .pdb)

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or specify the PDB accession code of the protein or protein complex (e.g. 1ABC)

(Optional) List the chains you want to analyse from the structure (space-separated, e.g. A B C)

To what field should the conservation values be added*

Multiple sequence alignment

(Optional) Upload one or more msa files (if more than one, coupled mode can't be used) (either .fasta, .a3m or .fa)

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Filter MSA for redundancy with hhfilter (sequence identity: [40%, 100%])

Take the top N closest sequences to the query (N: [20, 120])

Should the chains in the MSA be treated as a unit while sub-sampling the MSA? (coupled mode) By default, chains are split before MSA sub-sampling
This option applies only when there are several chains and if a single MSA file is given (AlphaFold output format) or if the MSA is generated by this server

Job name

(Optional) Give your job a name (max 30 characters)

Reset fields