MPI Bioinformatics Toolkit statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool MPI Bioinformatics Toolkit
info

Tool usage distribution map

This map represents all the scientific publications referring to MPI Bioinformatics Toolkit per scientific context
info info

Associated diseases

info

Popular tool citations

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
Want to access the full stats & trends on this tool?

Protocols

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 citations

 (28)
library_books

Phyletic Distribution and Lineage Specific Domain Architectures of Archaeal Two Component Signal Transduction Systems

2018
J Bacteriol
PMCID: 5847659
PMID: 29263101
DOI: 10.1128/JB.00681-17

[…] outputs. 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 an […]

library_books

The Global Acetylome of the Human Pathogen Vibrio cholerae V52 Reveals Lysine Acetylation of Major Transcriptional Regulators

2018
PMCID: 5768985
PMID: 29376036
DOI: 10.3389/fcimb.2017.00537

[…] al., ). 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 and […]

call_split

Human LINE 1 retrotransposition requires a metastable coiled coil and a positively charged N terminus in L1ORF1p

2018
eLife
PMCID: 5940361
PMID: 29565245
DOI: 10.7554/eLife.34960.037
call_split See protocol

[…] econstructed 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. […]

library_books

Complete Genome Sequencing of Mycobacterium bovis SP38 and Comparative Genomics of Mycobacterium bovis and M. tuberculosis Strains

2017
Front Microbiol
PMCID: 5723337
PMID: 29259589
DOI: 10.3389/fmicb.2017.02389

[…] 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) (Tat […]

call_split

Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double ring complex with unique inner cavity properties

2017
PMCID: 5777263
PMID: 29183996
DOI: 10.1074/jbc.M117.815258
call_split See protocol

[…] quences to be included for the next iteration were manually reviewed. The sequences resulting from each of the searches were filtered down to a pairwise sequence identity of 90% using HHfilter in the MPI Bioinformatics Toolkit (). The sequences in these reduced sets were next clustered by their all-against-all pairwise BLAST p values in CLANS () to identify and remove incomplete or unrelated seque […]

call_split

Characterization of the CrbS/R Two Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR Mediated Transcriptional Activation

2017
Front Microbiol
PMCID: 5715377
PMID: 29250042
DOI: 10.3389/fmicb.2017.02287
call_split See protocol

[…] was used. MEME (Bailey et al., ) and FIMO (Grant et al., ) searches were run with the default options searching for a motif between 6 and 30 nucleotides long. Sequence analyses were performed in the MPI bioinformatics toolkit (Alva et al., ; https://toolkit.tuebingen.mpg.de) using Quick2D, HHpred (Hildebrand et al., ), PCOILS (Lupas et al., ), and MARCOIL (Delorenzi and Speed, ). Transmembrane se […]


Want to access the full list of citations?
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].

MPI Bioinformatics Toolkit reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MPI Bioinformatics Toolkit