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ENCoM Server

ENCoM is a coarse grained normal modes analysis method to evaluate thermostability of proteins. The ENCoM Server can be used by anyone to evaluate the effect of mutations on the stability of a structure. The server can also generate geometrically realistic conformational ensembles.
Consult the guide
Cite: Frappier V., Chartier M. and Najmanovich R. (2015) ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability. Nucleic Acids Research. PubMed | NAR | PDF
Contact: Vincent.Frappier@USherbrooke.ca, Rafael.Najmanovich@USherbrooke.ca.
ENCoM Tutorial

Model combination scripts

Git Page
Effect of Mutations Conformational Sampling Guide

Effect of mutations

Here you can evaluate the effect of mutations on the thermodynamic stability of a structure. You can define the residue(s) of a specific protein chain and the mutations to evaluate at these positions. Mutant structures are generated with Modeller and the effect on thermodynamic stability is evaluated with ENCoM and FoldX.

See the adenylate kinase example - From the PDB structure 4AKE, the effect of mutations at positions 10 to 15 of chain A for glutamine, alanine, leucine and glycine (input at step 3: '10-15 A Q,A,L,G') was evaluated.


Job Submission Form

For help please consult the Guide.

1. Input structure

Enter a PDB code: | Or upload a PDB file:

2. Chains (optional)

To evaluate the impact of the mutation(s), ENCoM can use specific chains of the PDB structure. Leave blank for all chains or enter comma separated chains (e.g.: A,B,C)


3. Mutation(s)

Three elements are needed to specify which mutations to evaluate:
  1. A residue number or range: 25 or 1-10
  2. The chain of the residues specified: B
  3. The amino-acids to mutate to (one letter code and comma separated if many): D or all for all mutations
1-10 B A,D - This tells ENCoM to evaluate the impact of mutating individually residues 1 to 10 of chain B to Alanines (A) and Aspartates (D).

Add as many mutations as needed by separating them with a semi-colon (;): 1-10 B A,D; 25 A all


4. Email notification (optional)

If desired, an email will be sent upon job submission with a link to the results page. A second email will be sent upon termination.