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Protocols

ENCoM specifications

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Unique identifier OMICS_08059
Name ENCoM
Alternative name Elastic Network Contact Model
Interface Web user interface
Restrictions to use None
Input format PDB
Computer skills Basic
Stability Stable
Maintained No

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Information


Unique identifier OMICS_08059
Name ENCoM
Alternative name Elastic Network Contact Model
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
Computer skills Advanced
Stability Stable
Maintained No

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Publications for Elastic Network Contact Model

ENCoM citations

 (11)
library_books

Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae

2018
Sci Rep
PMCID: 5864748
PMID: 29567948
DOI: 10.1038/s41598-018-23423-1

[…] mol of change in energy (measured using mCSM-ppi). ENCoM and FoldX4 programs predicted destabilizing energy changes in RNAP in the presence of all the four mutations. By generating normal modes using elastic network contact model and calculating the vibrational entropy and enthalpy changes in the system, it was noted that the current mutations impact the thermodynamic properties of RNAP and has po […]

library_books

A computational study for rational HIV 1 non nucleoside reverse transcriptase inhibitor selection and the discovery of novel allosteric pockets for inhibitor design

2018
Biosci Rep
PMCID: 5835713
PMID: 29437904
DOI: 10.1042/BSR20171113

[…] erage coupling’ concept (refer to Goncearenco et al. [] for more details) in SPACER.Structural thermal stability: Thermal stability of the modeled RT–NNRTI complex structures were evaluated using the ENCoM [] (standalone version; according to the protocol []) with the wild-type control (PDB: 3T19) for the corresponding mutations. The estimated free energy change (ΔΔG including vibrational entropy […]

library_books

Experimental Determination and Prediction of the Fitness Effects of Random Point Mutations in the Biosynthetic Enzyme HisA

2017
Mol Biol Evol
PMCID: 5850734
PMID: 29294020
DOI: 10.1093/molbev/msx325

[…] tations were excluded (henceforth referred to as the nonlethal model). A model built by including the lethal mutations with 8 different predictors (EASE-MM ΔΔG, I-Mutant ΔΔG, NeEMO ΔΔG, PoPMuSiC ΔΔG, ENCoM ΔΔG, SDM ΔΔG, Secondary structure and face location [catalytic or stability face]; C and D, online; henceforth referred to as the lethal model) explained 50% of the observed variance. Thus, by […]

library_books

In silico model of the human ClC Kb chloride channel: pore mapping, biostructural pathology and drug screening

2017
Sci Rep
PMCID: 5543074
PMID: 28775266
DOI: 10.1038/s41598-017-07794-5

[…] ENCoM predicts the effect of mutations on the protein dynamics. It has been shown that combining the ENCoM predictions with those from FoldX3.0 increase substantially the prediction accuracy. Indeed, ENCoM is more focused on the prediction of the entropy gain or loss, whereas FoldX is more focused on questions related to enthalpy.The ClC-Kb mutants or variants were generated using the psfgen packa […]

library_books

Computing disease linked SOD1 mutations: deciphering protein stability and patient phenotype relations

2017
Sci Rep
PMCID: 5498623
PMID: 28680046
DOI: 10.1038/s41598-017-04950-9

[…] e methods ordered according to their ascending MAEs is: PoPMuSiC 3.1 (1.08 kcal/mol) < FoldX (1.1 kcal/mol) < I-Mutant 2.0 (1.17 kcal/mol) ~ I-Mutant 3.0 (1.17 kcal/mol) ~ BeatMusic (1.17 kcal/mol) < ENCoM (1.5 kcal/mol) < CUPSAT (1.81 kcal/mol) ≪ mCSM (3.2 kcal/mol). This order resembles what has been reported earlier by Kepp, , though he didn’t include all these predictors.In case of apo-monomer […]

library_books

Geochemistry and mineralogy of the Oligo Miocene sediments of the Valley of Lakes, Mongolia

2017
PMCID: 5367698
PMID: 28450967
DOI: 10.1007/s12549-016-0268-6

[…] circulating hydrothermal fluids generated during post-Oligocene basalt flood event(s). This hydrothermal circulation resulted in a significant post-depositional alteration and in an accompanying all encom-passing homogenization of the mineralogical and major element composition of the entire Eocene to Miocene succession. The trace element composition, i.e. Th/Sc and Zr/Sc ratios, however, reveals […]


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ENCoM institution(s)
Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada; Department of Computer Science and Operations Research, Université de Montréal, Montréal, QC, Canada; Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada; Department of Pharmacology and Physiology, Université de Montréal, Montréal, QC, Canada; Department of Biology, MIT, Cambridge, MA, USA
ENCoM funding source(s)
Supported by Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery program grants and Canadian Institutes of Health Research (CIHR) (grant number MOP-93679).

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