The server lets users mutate proteins in various ways and study mutation effects in 3D. The only required inputs are a structural model and a list of mutations of interest. Alternatively, the user can upload human SNPs in the VCF format.
You can click on the i buttons at each field in the forms to get further information.

Main steps

Either:

• create an alignment on AlignMe webserver
• forward the results to MutationExplorer
• select base and target sequence
• upload base (and optionally target) structure
• get homology model (or optionally superimposed models)

Or:

• upload human SNPs in VCF format

Or:

• upload structure
• define mutations

Always:

• explore: mutate again and again ...
• mutation forecast using RaSP
• color by:   absolute/differences     energy/hydrophobicity/conservation

Structure upload

Structures can be uploaded in three different ways:

• PDB ID,
• AlphaFold ID
• upload local PDB file

Define mutations

Mutations can be defined in three different ways:

• key or paste into GUI, using a simple syntax: [chain]:[residue number][target mutation], example: ”A:12G,B:134T". The residue number has to be present in and match the uploaded PDB
• upload alignment in ClustalW format
• upload target sequence either by pasting the sequence, uploading a FASTA file or specifying a Uniprot ID

Mutation syntax

• a comma separated list of CHAIN ':' RESIDUE-ID TARGET-AA-TYPE
• example: 'A:23G,B:123A'
• this mutates the residue in chain A with the PDB residue ID 23 to glycine and in chain B the residue with residue ID 123 to alanine

Explorations

You can select a model and further mutate this using the mutation window.

Expected time requirements

Actual times depend on the size of the system and may vary significantly.

• initial basic minimization: 1-3 min
• per round of mutations: ~2 min
• VCF processing (plus minimization): 5 min

Details can be found in the FAQs.