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Information


Unique identifier OMICS_27786
Name MinDist
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Maintained No

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Publication for MinDist

MinDist citations

 (68)
library_books

Interaction of lecithin:cholesterol acyltransferase with lipid surfaces and apolipoprotein A I derived peptides[S]

2018
J Lipid Res
PMCID: 5880497
PMID: 29438987
DOI: 10.1194/jlr.M082685

[…] e maximum angle formed by hydrogen bonding atoms hydrogen-donor-acceptor was set to 30 degrees. The number of salt bridges in the structure of LCAT concerning the lid-region was calculated by the gmx mindist program with a distance criterion of 0.6 nm between the charged side chain central carbon atoms of negatively and positively charged amino acids (GLU-ARG, GLU-LYS, ASP-ARG, and ASP-LYS). The s […]

library_books

The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages

2018
Immunity
PMCID: 5772169
PMID: 29343442
DOI: 10.1016/j.immuni.2017.12.010

[…] th default parameters. MACS2 () (with ‘-B’ and ‘-SPMR’ options) was used for predicting transcription factor peaks and nucleosome free regions (q-value ≤ 0.01), and findPeaks.pl (with ‘-size 1000’, ‘-minDist 2500’ and ‘-style histone’ options) for histone regions. Artifacts were removed using the ENCODE blacklist (). Predicted peaks were sorted by average coverage (RPKM, Reads Per Kilobase per Mil […]

library_books

LSD1 activation promotes inducible EMT programs and modulates the tumour microenvironment in breast cancer

2018
Sci Rep
PMCID: 5758711
PMID: 29311580
DOI: 10.1038/s41598-017-17913-x

[…] es were created from the first read using HTSEQ. Enriched regions were called against Total Input with the first read of the pair using HOMER (-fragLength 200 findPeaks -style histone -F 4 -size 300 -minDist 300) and then filtered so that each region had at least 12.2 normalised reads. HOMER was used to annotate and profile the regions, search for enriched motifs and ontology, count tags in the re […]

library_books

Mechanistic insights into remodeled Tau derived PHF6 peptide fibrils by Naphthoquinone Tryptophan hybrids

2018
Sci Rep
PMCID: 5758761
PMID: 29311706
DOI: 10.1038/s41598-017-18443-2

[…] To identify the mechanism behind NQTrp and Cl-NQTrp interaction with the PHF6 oligomer, we calculated the evolution of hydrogen bonds during simulation using g_hbond and number of interaction using g_mindist. As the number of interaction increased, (Supplementary Fig. ) single molecule of NQTrp or Cl-NQTrp formed an average of 1–2 hydrogen bonds with the peptide oligomer (Fig. ).Figure 5 Experimen […]

library_books

Transcriptomes define distinct subgroups of salivary gland adenoid cystic carcinoma with different driver mutations and outcomes

2017
Oncotarget
PMCID: 5800907
PMID: 29484115
DOI: 10.18632/oncotarget.23641

[…] measures described in the text. Peak finding to identify samples that expressed MYB or MYBL1 was performed using findpeaks from the HOMER (v4.9) package [], with settings of -region, -size 1000 and -minDist 10000. […]

library_books

Structure and Interactions of A Host Defense Antimicrobial Peptide Thanatin in Lipopolysaccharide Micelles Reveal Mechanism of Bacterial Cell Agglutination

2017
Sci Rep
PMCID: 5736615
PMID: 29259246
DOI: 10.1038/s41598-017-18102-6

[…] among cationic sidechains. The dimer structure is only stabilized in complex with LPS. The minimum distance and center of mass distance between LPS and thanatin dimer were calculated using Gromacs g_mindist and g_dist respectively. The coordination number (CN) of LPS/thanatin was defined as2CN=∑i=1NLPS∑j=1NthanC(dij)and3C(dij)={1,dij≤cutoff0,dij>cutoffwhereas, NLPS and Nthan are the total number […]

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MinDist institution(s)
Equipe BAOBAB, Laboratoire de Biometrie et Biologie Evolutive (UMR 5558), CNRS, University of Lyon 1, Villeurbanne, France; INESC-ID/IST, Lisbon, Portugal; BAMBOO Team, INRIA Rhone-Alpes, Montbonnot Saint-Martin, France; Instituto Gulbenkian de Ciencia, Oeiras, Portugal; Department of Computer Science, University of Freiburg, Freiburg, Germany; Center for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany; Center for Non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
MinDist funding source(s)
Supported by FCT—Fundacao para a Ciencia e a Tecnologia (INESC-ID multiannual funding) through the PIDDAC Program funds, the PTDC program [PTDC/AGR-GPL/ 098179/2008] and under project [PEst-OE/EEI/LA0021/2011], the Agence Nationale de la Recherche [BRASERO project BLAN06-3 138859, MIRI project BLAN08-1 335497]; the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement no [247073]10, the German Research Foundation [DFG grants BA 2168/3-1, BA 2168/4-1], and the Excellence Initiative of the German Federal and State Governments [grant EXC 294].

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