MPI Bioinformatics Toolkit protocols

View MPI Bioinformatics Toolkit computational protocol

MPI Bioinformatics Toolkit statistics

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chevron_left Phylogenetic inference Secondary structure prediction Tertiary structure prediction Multiple amino acid sequence alignment Coiled-coil domain prediction Protein sequence reconstruction Protein clustering Hydrophobic region prediction chevron_right
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MPI Bioinformatics Toolkit specifications

Information


Unique identifier OMICS_24479
Name MPI Bioinformatics Toolkit
Software type Toolkit/Suite
Interface Web user interface
Restrictions to use None
Input data A DNA sequence.
License GNU Lesser General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Andrei Lupas <>
  • person_outline Vikram Alva <>

Publications for MPI Bioinformatics Toolkit

MPI Bioinformatics Toolkit in pipelines

 (2)
2017
PMCID: 5627817
PMID: 28746191
DOI: 10.1097/MD.0000000000007490

[…] structure-based threading server phyre[] to generate the cngb3 model, taking the eag1 crystal structure (pdb id: 5k7l chain a) as a template. all sequence similarity searches were carried out in the mpi bioinformatics toolkit using hhpred[] with default settings. hhpred searches for template were performed against a database comprising pdb70 (protein databank structures, as available on january […]

2016
PMCID: 5025540
PMID: 27695441
DOI: 10.3389/fmicb.2016.01431

[…] an abi 377 automated sequencer. chimeric sequences of 16s rrna gene sequences were excluded by bellerophon (). valid sequences with more than 97% similarity were classified through the blastclust of mpi bioinformatics toolkit () to arrive operational taxonomic unit (otu). functional genes were translated through expasy translation tool. sequences were compared to the genbank nucleotide sequence […]


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MPI Bioinformatics Toolkit in publications

 (27)
PMCID: 5847659
PMID: 29263101
DOI: 10.1128/JB.00681-17

[…] these putative novel output domains were compared against arcogs and further analyzed for remote sequence similarity using the cd search () with relaxed cutoffs and the hhpred tool () of the mpi bioinformatics toolkit () (table s5). protein secondary structures were taken from the hhpred outputs and/or predicted using jpred (). putative novel output domains were assigned mnemonic names […]

PMCID: 5805765
PMID: 29422648
DOI: 10.1038/s41467-017-02646-2

[…] for proteins without annotation or predicted function/location, domain prediction based on protein homology is presented in square brackets where available (hhpred protein prdomain prediction, the mpi bioinformatics toolkit as an integrative platform for advanced protein sequence and structure analysis), tm:┬átransmembrane domains (tmhmm: plasmodb, pmid1115261. credits: anders krogh, bjorn […]

PMCID: 5768985
PMID: 29376036
DOI: 10.3389/fcimb.2017.00537

[…] ). a 21 amino acid sequence window was chosen, the compiled v. cholerae v52 proteome was used as background, and otherwise default settings were applied. homology models were generated using the mpi bioinformatics toolkit (alva et al., ). protein sequences were submitted to hhpred and the five top hits were forwarded to modeler in order to obtain the homology models. figures of structures […]

PMCID: 5940361
PMID: 29565245
DOI: 10.7554/eLife.34960.037

[…] megabat sequence (ncbi kf796623.1) is from yang et al. (). individual accession numbers for the reconstruction of primate l1orf1p sequences are listed in . pcoils () as integrated in the mpi bioinformatics toolkit () and iupred () were used for assigning coiled coil propensity and the probability of disorder, respectively., the dna sequences encoding purified fragments of the human […]

PMCID: 5723337
PMID: 29259589
DOI: 10.3389/fmicb.2017.02389

[…] and deletion of spoligotype spacer 21 for european 2 (rodriguez-campos et al., )., paralogous gene families (pgf) of m. bovis strain sp38 were identified using blastclust, available online in the mpi bioinformatics toolkit (alva et al., ). parameters of 70% coverage and 30% of identity were used. pgf were separated into functional categories according to cog (cluster of orthologous group) […]


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MPI Bioinformatics Toolkit institution(s)
Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen, Germany; Group for Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
MPI Bioinformatics Toolkit funding source(s)
Supported by Institutional funds of the Max Planck Society; German Federal Ministry of Education and Research (BMBF) within the framework of e:Med [e:AtheroSysMed, 01ZX1313A-2014] and e:bio [SysCore].

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