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Protocols

DAMMIF specifications

Information


Unique identifier OMICS_22841
Name DAMMIF
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.1.2
Stability Stable
Requirements
ATSAS
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Dmitri I. Svergun
  • person_outline Daniel Franke

Publications for DAMMIF

DAMMIF citations

 (261)
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Conformational sampling of membranes by Akt controls its activation and inactivation

2018
Proc Natl Acad Sci U S A
PMCID: 5924885
PMID: 29632185
DOI: 10.1073/pnas.1716109115
call_split See protocol

[…] ring curves [I(q) vs. q] in an automatic, unbiased manner. Ab initio molecular envelopes for Akt1DrLink were computed by 10 iterative cycles of simulated annealing starting with a dummy atom model in DAMMIF (). The models were aligned, averaged, and filtered using DAMAVER (). The structure of Akt11−443 in complex with inhibitor VIII (PDB ID code 3O96) was compared with the scattering of Akt1DrLink […]

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

[…] ons using standard procedures and program PRIMUS []. The resultant curves were used for all calculations and reconstructions. Low resolution shapes of PgdS were reconstructed by the ab initio method, DAMMIF []. Twenty models obtained from the program runs were compared and averaged using the program DAMAVER [], with the most universal model was chosen as typical model. Currently, the high resoluti […]

library_books

Structural insights into the RNA methyltransferase domain of METTL16

2018
Sci Rep
PMCID: 5871880
PMID: 29593291
DOI: 10.1038/s41598-018-23608-8

[…] IMUS and GNOM for calculation of the radius of gyration (Rg) and the pair distribution function, P(r). Molecular masses are based on the calculation of low-resolution ab initio models with the use of DAMMIF, DAMAVER, DAMMIN, and DAMFILT. […]

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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

[…] serum albumin, the hydrated-particle/Porod volume Vp, where molecular mass 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 unconstrai […]

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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

[…] gether with the fitting of the calculated scattering curve from each ensemble to the experimental SAXS data. The calculation of ab initio shapes based on the scattering data was done with the program DAMMIF from the ATSAS package (). Table S4 shows all the SAXS-derived parameters. […]

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

[…] Low resolution shapes were reconstructed from SAXS data using the programs DAMMIF, which represents the macromolecule as a densely packed interconnected configuration of beads or chain-like ensemble of dummy residues, respectively, that best fits the experimental data Iexp(s […]

Citations

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DAMMIF institution(s)
European Molecular Biology Laboratory, Hamburg, Germany; Institute of Crystallography, Moscow, Russia
DAMMIF funding source(s)
Supported by EU FP6 Design study SAXIER, grant No. RIDS 011934.

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