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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
Job Infos
PDB:4AKE ADENYLATE KINASE
Chain(s) kept: A
Mutation(s):
10-15 A Q,A,L,G

Downloads
sessions.zip - Structures coloured based on the effect of the mutation (red more flexible, blue more rigid)
models.zip - Modelled mutant structures
seq_tolerance.pdf - Heatmap of the effect of each mutation on the sequence
top25_graph.pdf - Top 25 stabilizing mutations and their effect on sequence
all_ddg.csv - Predicted ΔΔG of each mutation at each residue
all_graph.pdf - All graphs of the effect of mutations on sequence

For more info, consult the Guide
Log

>[NRG cluster]$ Status for job exampleMut

Generated Mon Mar 23 10:17:03 EDT 2015

100.0 percent complete

Depending of the server load, estimated time to complete the job for 20 mutation(s) and a protein of 214 amino acids is between 0.1 and 1.2 hours

Modelling mutations... 20 mutation(s) modelled
Evaluating energy with ENCoM...20 mutation(s) evaluated
Evaluating energy with FoldX...20 mutation(s) evaluated
Generating Figures... 20 figure(s) generated


Job finished!
Runtime was 13.63 minutes
Mutation(s) predicted to have a significant effect
A GIF or PNG of the structure coloured based on the effect of the mutation (red more flexible, blue more rigid) is available for each mutant. Download a PML script to view the colored structures in PyMol or download the mutant structure.

# WT Residue Res. # Chain Mutation ENCoM
ΔkCal/mol
desc asc
FoldX3.0
ΔkCal/mol
desc asc
Combined
ΔkCal/mol
desc asc
GIFPNG Pymol
Session
PDB
1LYS 13 A LEU -0.29 -0.17 -0.45 GIF PNGPMLPDB
2GLY 14 A GLN -0.05 -0.23 -0.27 GIF PNGPMLPDB
3GLY 14 A LEU -0.12 -0.07 -0.19 GIF PNGPMLPDB
4GLY 14 A ALA 0.00 -0.09 -0.09 GIF PNGPMLPDB
5THR 15 A LEU -0.02 -0.04 -0.06 GIF PNGPMLPDB
6THR 15 A GLN 0.01 0.04 0.05 GIF PNGPMLPDB
7LYS 13 A GLN 0.11 0.07 0.19 GIF PNGPMLPDB
8THR 15 A ALA 0.29 0.06 0.35 GIF PNGPMLPDB
9ALA 11 A LEU -0.51 0.89 0.38 GIF PNGPMLPDB
10ALA 11 A GLN -0.93 1.51 0.58 GIF PNGPMLPDB
11LYS 13 A ALA 0.63 -0.01 0.62 GIF PNGPMLPDB
12ALA 11 A GLY 0.27 0.61 0.88 GIF PNGPMLPDB
13GLY 10 A LEU -0.39 1.29 0.90 GIF PNGPMLPDB
14GLY 12 A GLN -0.06 0.97 0.91 GIF PNGPMLPDB
15THR 15 A GLY 0.72 0.25 0.97 GIF PNGPMLPDB
16GLY 12 A ALA 0.02 1.01 1.03 GIF PNGPMLPDB
17GLY 12 A LEU -0.05 1.31 1.26 GIF PNGPMLPDB
18LYS 13 A GLY 1.03 0.47 1.49 GIF PNGPMLPDB
19GLY 10 A GLN -0.24 1.79 1.54 GIF PNGPMLPDB
20GLY 10 A ALA -0.10 1.86 1.76 GIF PNGPMLPDB