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Protocols

DAMMIN specifications

Information


Unique identifier OMICS_29291
Name DAMMIN
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 5.3
Stability Stable
Requirements
ATSAS
Registration required Yes
Maintained Yes

Maintainer


  • person_outline Daniel Franke

Additional information


https://www.embl-hamburg.de/biosaxs/manuals/dammin.html

Publications for DAMMIN

DAMMIN citations

 (207)
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

[…] 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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Insc:LGN tetramers promote asymmetric divisions of mammary stem cells

2018
Nat Commun
PMCID: 5844954
PMID: 29523789
DOI: 10.1038/s41467-018-03343-4
call_split See protocol

[…] he ATSAS package. 20 ab initio models for both P1 and P2 symmetry were calculated using DAMMIF, and then averaged, aligned and compared using DAMAVER. A representative bead model was calculated using DAMMIN, and aligned to the crystallographic structures using SUPCOMB and PyMol. Theoretical scattering curves of the known dLGNTPR:InscASYM structures were calculated and fitted to the experimental cu […]

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The H subunit of the restriction endonuclease CglI contains a prototype DEAD Z1 helicase like motor

2018
Nucleic Acids Res
PMCID: 5861437
PMID: 29471489
DOI: 10.1093/nar/gky107
call_split See protocol

[…] at PETRA III storage ring of DESY synchrotron in Hamburg (Germany). The SAXS data collection parameters and processing for H.CglI sample were described in (). Dummy atoms models were calculated with DAMMIN (version 5.3) () and DAMMIF (r6669) () applying P1 or P2 symmetry, as the molecular weight of H.CglI in solution corresponds to dimer (). Both variants, P1 and P2 were very similar. Ten runs of […]

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Structure of prothrombin in the closed form reveals new details on the mechanism of activation

2018
Sci Rep
PMCID: 5811608
PMID: 29440720
DOI: 10.1038/s41598-018-21304-1
call_split See protocol

[…] e beamline 12-ID-B of the Advanced Photon Source at Argonne National Laboratory (Argonne, IL) on protWT (0.5–5 mg/ml). The low-resolution envelope was produced using both GASBOR (q up to 0.8 Å−1) and DAMMIN (q up to 0.3 Å−1) by directly fitting the reciprocal space scattering profile. Twenty models were generated for every calculation and then aligned and averaged using DAMAVER. Computing of the t […]

library_books

CPAP3 proteins in the mineralized cuticle of a decapod crustacean

2018
Sci Rep
PMCID: 5799365
PMID: 29403068
DOI: 10.1038/s41598-018-20835-x

[…] sed to obtain pair-distance distribution functions and the corresponding maximum dimension of the protein complexes (Dmax), as described by Svergun. An ab initio envelope was generated by the program DAMMIN Svergun, using atomic radii set to the dummy atom packing radius determined by DAMMIN without imposing a symmetry operation. The generated envelope model (DBM) was fitted on the core structure […]

library_books

SAXS analysis of a soluble cytosolic NgBR construct including extracellular and transmembrane domains

2018
PLoS One
PMCID: 5773207
PMID: 29346419
DOI: 10.1371/journal.pone.0191371

[…] mation. Pair distribution function (P(r)) and the maximum particle dimension (Dmax) were estimated from the scattering data using the GNOM algorithm. An ab initio dummy atom model was generated using DAMMIN []. The molecular weight (MW) of the model was estimated by taking the volume from the model and dividing it by 2 []. The theoretical scattering curve of the UPPs (undecaprenyl pyrophosphate sy […]

Citations

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DAMMIN institution(s)
European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany; Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Moscow, Russia; 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
DAMMIN 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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