FiltRest3D specifications

Information


Unique identifier OMICS_13704
Name FiltRest3D
Interface Application programming interface
Restrictions to use None
Input data User can upload PDB files directly or it is advised to pack your PDB files into .ZIP file.
Input format PDB, ZIP
Computer skills Advanced
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Janusz Bujnicki <>

Publication for FiltRest3D

FiltRest3D in publications

 (4)
PMCID: 4737155
PMID: 26673726
DOI: 10.1093/nar/gkv1369

[…] particular for experimental validation., using additional data from emsa and activity measurements of trm10 variants, we filtered models from the three obtained clusters. in particular, we applied filtrest3d () to find a model that fulfils all distance restraints inferred from experimental analyses. this filtering procedure revealed that a highly-scored model from the second cluster […]

PMCID: 4152360
PMID: 24785264
DOI: 10.4161/rna.28826

[…] and used to identify “good” structures among a set of models generated by essentially any modeling method. for discrimination of models that agree with experimental data we can recommend e.g., the filtrest3d method developed in our group and available as a standalone program as well as a web server., the second most common group of restraints used for rna 3d modeling are ones encoded […]

PMCID: 3200286
PMID: 22091405
DOI: 10.4061/2011/475718

[…] dataset of protein-dna complexes that can be used for benchmarking purposes []. an alternative approach is to build models with other methods, without the use of experimental data, and then use the “filtrest3d” method developed in the laboratory of the authors [] to rank them according to the extent of agreement with the restraints., as illustrated by the example of the mlh1 protein, prediction […]

PMCID: 3061052
PMID: 21062819
DOI: 10.1093/nar/gkq1033

[…] repulsion and attraction were 30 and 0, respectively, grid size 64 å, grid step 2.8 å. the npma structure was rotated with 10° angle intervals. subsequently, all 10 000 poses were filtered using the filtrest3d server (), to rank them according to the proximity of the n1 atom of a1408 and the methyl group of adomet bound to npma. top 100 variants have been clustered with maxcluster […]


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FiltRest3D institution(s)
International Institute of Molecular and Cell Biology, Warsaw, Poland; European Molecular Biology Laboratories, Hamburg Outstation, Hamburg, Germany; PhD School, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland; The State Research Center of Virology and Biotechnology VECTOR, Novosibirsk, Russia; Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
FiltRest3D funding source(s)
This work was supported by Polish Ministry of Science and Higher Education (grants HISZPANIA/152/2006 and POIG.02.03.00-00-003/09); the National Institutes of Health (R01-GM081680); European Commission (LSHG-CT-2005-518238, 229676 and RIDS-011934); Human Frontier Science Program (RGP 55/2006).

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