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Protocols

GBIS specifications

Information


Unique identifier OMICS_21012
Name GBIS
Alternative name Genebank Information System
Restrictions to use None
Database management system Oracle
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Markus Oppermann
  • person_outline GBIS team

Additional information


https://gbis.ipk gatersleben.de/GBIS_I/home.jsf;jsessionid=NhR6gHcrbzkhYKE1jg60YsdbDxGD-2wM9Z5sTZ1c8dIgco2u8AJ6!1505460084!1505293793067

Publication for Genebank Information System

GBIS citations

 (10)
library_books

De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads

2018
BMC Biol
PMCID: 5765664
PMID: 29325570
DOI: 10.1186/s12915-017-0473-4

[…] tie2 -p 10 --no-unal --no-mixed --local -x 10k_called_A_132394_albacore_1.1.0.fa -1 <(pv ~/bioinf/MIMR-2017-Jan-01-GBIS/GLG/ONT/aws/Sampled_50M_ERR063640.R1.fq.gz | zcat) -2 ~/bioinf/MIMR-2017-Jan-01-GBIS/GLG/ONT/aws/Sampled_50M_ERR063640.R2.fq.gz | samtools sort > WTSI_Sampled_50M_vs_10k_called_A_132394.bam ## find position of first mapped Illumina read for each nanopore read pv WTSI_Sampled_50 […]

call_split

Adsorption of Milk Proteins (β Casein and β Lactoglobulin) and BSA onto Hydrophobic Surfaces

2017
PMCID: 5578259
PMID: 28767100
DOI: 10.3390/ma10080893
call_split See protocol

[…] We have performed molecular dynamics (MD) simulations of the proteins of interest using the GBIS model described above as implemented in NAMD Version 2.9 []. Newton’s equations of motion were solved with a time step of 2 fs, and electrostatic interactions were updated with a 4-fs time step ( […]

library_books

Neuron specific knock down of SMN1 causes neuron degeneration and death through an apoptotic mechanism

2016
Hum Mol Genet
PMCID: 5181630
PMID: 27260405
DOI: 10.1093/hmg/ddw119

[…] punc-25::kal-1 RNAi HC], gbEx588[punc-25::unc-70 RNAi MC], gbEx529[punc-119::hSMN1], gbEx540[punc-119::DsRed2], gbEx580[punc-25::smn-1 RNAi HC], gbEx581[punc-25::smn-1 RNAi HC], gbEx612[pchs-2::GFP], gbIs4[punc-25::smn-1 RNAi HC], vdIs4[punc-25::ChFP::RAB-3]. A full description of the transgenes is available in the Supplementary Material, Supplementary Methods section. Genetic crosses were made to […]

library_books

Multi kinase inhibitors interact with sildenafil and ERBB1/2/4 inhibitors to kill tumor cells in vitro and in vivo

2016
Oncotarget
PMCID: 5130016
PMID: 27259258
DOI: 10.18632/oncotarget.9752

[…] Initial CGenFF-compatible parameters for the pazopanib were derived using the CGenFF website and subsequently optimized. Subsequently, 50 ns of accelerated MD with Generalized Born Implicit Solvent (GBIS) for both HSP90 in complex with pazopanib and apo-HSP90 was performed. […]

library_books

Multi kinase inhibitors can associate with heat shock proteins through their NH2 termini by which they suppress chaperone function

2016
Oncotarget
PMCID: 4914336
PMID: 26887051
DOI: 10.18632/oncotarget.7349

[…] run. Initial CGenFF-compatible parameters for the AR-12 were derived using the CGenFF website and subsequently optimized. Subsequently, 50 ns of accelerated MD with Generalized Born Implicit Solvent (GBIS) for both HSP90 in complex with AR-12 and apo-HSP90 was performed [–]. […]

library_books

Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers

2015
PLoS One
PMCID: 4575034
PMID: 26382062
DOI: 10.1371/journal.pone.0138392

[…] ns of each MD trajectory of the dendrimer, DNA and complex dendrimer-DNA systems. Polar contributions to the solvation free energy (Gsolv-p) were solved using the Generalized Born approach, using the GBIS module included in NAMD, as a post-processing analysis of the MD trajectories. Non-polar contribution (Gsolv-np) was calculated as a linear function of the solvent-accessible surface area (SASA), […]


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GBIS institution(s)
Leibniz-Institut fur Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Gatersleben, Germany
GBIS funding source(s)
Initially supported by the German Federal Ministry of Education and Research and the German Federal Ministry of Food and Agriculture.

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