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EOM specifications

Information


Unique identifier OMICS_29096
Name EOM
Alternative name Ensemble Optimization Method
Interface Web user interface
Restrictions to use None
Computer skills Basic
Registration required Yes
Maintained Yes

Maintainers


  • person_outline Dmitri I. Svergun
  • person_outline Daniel Franke

Information


Unique identifier OMICS_29096
Name EOM
Alternative name Ensemble Optimization Method
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 2.0
Requirements
ATSAS
Registration required Yes
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Dmitri I. Svergun
  • person_outline Daniel Franke

Publications for Ensemble Optimization Method

EOM citations

 (132)
library_books

Solution scattering study of the Bacillus subtilis PgdS enzyme involved in poly γ glutamic acids degradation

2018
PLoS One
PMCID: 5880399
PMID: 29608608
DOI: 10.1371/journal.pone.0195355

[…] units. The program CORAL [] was used to reconstruct missing fragments of the available high-resolution structures using the full amino acid sequences. Considering the flexibility of proteins, program EOM [] was also used to analyze the PgdS enzyme with assemblies of different conformers. […]

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Structural Basis for Draxin Modulated Axon Guidance and Fasciculation by Netrin 1 through DCC

2018
Neuron
PMCID: 5871715
PMID: 29503192
DOI: 10.1016/j.neuron.2018.02.010
call_split See protocol

[…] ss is estimated as 0.588 times (Vp,) and from the excluded solvent volume (Vex) obtained from ab initio modeling in the program DAMMIF (). Ensemble analysis of hDraxin was conducted using the program EOM () using the c-terminal domain of rDraxin (rDraxin-C, this work) as a fixed rigid body and the remaining sequence unconstrained. Theoretical scattering profiles for compact and folded hDraxin, and […]

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Phosphorylation decelerates conformational dynamics in bacterial translation elongation factors

2018
Sci Adv
PMCID: 5851678
PMID: 29546243
DOI: 10.1126/sciadv.aap9714
call_split See protocol

[…] models were relaxed by molecular dynamics equilibration at 300 K (see below for further details), and sampling from the trajectory generated an initial ensemble of a few thousand models. We then used EOM (Ensemble Optimization Method) () and MES (Minimal Ensemble Search) () to select from this pool of structures the minimal ensembles with the best agreement with the experimental SAXS scattering cu […]

library_books

Structural model of human dUTPase in complex with a novel proteinaceous inhibitor

2018
Sci Rep
PMCID: 5847570
PMID: 29531348
DOI: 10.1038/s41598-018-22145-8

[…] the Stl model as the dimer interface based on our chemical crosslinking results (Supplementary Fig. ). An additional assessment of Stl protein flexibility based on a dimeric assembly determined using EOM, where a genetic algorithm is used to select an ensemble of best fitting configurations from a randomly generated pool. The program CORAL was used to perform a multi-step rigid body refinement of […]

library_books

Molecular Role of Ca2+ and Hard Divalent Metal Cations on Accelerated Fibrillation and Interfibrillar Aggregation of α Synuclein

2018
Sci Rep
PMCID: 5789889
PMID: 29382893
DOI: 10.1038/s41598-018-20320-5

[…] s performed to match our SAXS and IM-MS data. Representative structures of αSyn in solution were obtained from the structure pool of αSyn generated using replica exchange MD simulations, based on the ensemble optimization method (EOM), which identifies the best ensemble by fitting sum of multiple theoretical SAXS profiles to the experimental SAXS profile,. Using the obtained representative structu […]

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Combined roles of ATP and small hairpin RNA in the activation of RIG I revealed by solution based analysis

2018
Nucleic Acids Res
PMCID: 5887321
PMID: 29346611
DOI: 10.1093/nar/gkx1307
call_split See protocol

[…] ng using MONSA (). Normalized Kratky plots were calculated using the DATGNOM fitted scattering curves with a script written by MCJW. For analyses of the complexes of FL-RIG-I with 10 bp and 8 bp, the ensemble optimization method (EOM) () was used. […]

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EOM institution(s)
European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany; Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Moscow, Russia; A. N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Moscow, Russia; N.N. Semenov Institute of Chemical Physics of Russian Academy of Sciences, Moscow, Russia; National Research Centre ‘Kurchatov Institute’, Moscow, Russia; Department of Chemical Engineering, Stanford University, Stanford, CA, USA
EOM funding source(s)
Supported by FP7 Research Infrastructures (award Nos. Biostruct-X [283570], IDPbyNMR [264257], iNEXT [653706]); BMBF (award Nos. BIOSCAT [05K12YE1], TT-SAS [05K16YEA]); HFSP (award No. RGP0017/2012); DFG/GACR (award No. 9/5-1).

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