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3421 Data files visible to you, out of a total of 5622

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the M-loop region of a Trypanosoma brucei alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the M-loop region residue Leu286 (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-5 and 7-9, docked to the interface region between two neighboring alpha-tubulin monomers of Trypanosoma brucei; alpha-tubulin homology models were built on PDB-ID 5ubq and two monomeric models were aligned to neighboring protofilamentsof the original PDB-ID 5ubq to construct an interface-model receptor. The docking grid was centered on the M-loop region residue ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the N-loop region of a Trypanosoma brucei alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the N-loop region residue Phe49 (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger ...

Trypanosoma brucei multimeric alpha-tubulin protein receptor for docking studies, generated by alignment of two identical models of T. brucei alpha-tubulin on template 5ubq alpha-tubulin chains of two neighboring protofilaments (A, C).

Zip-archive with top-ranked (by IFDScore) induced fit docking results for dinitroaniline etherphospholipid hybrid compounds 1, 2, 4, 5 and 9 and reference compound trifluraline, docked to the Blume site of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on site residue Ala4 (T. cruzi numbering). No results were obtained with compounds 3 and 6-8.

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compounds 1, 4, 8 and reference compound trifluraline, docked to the Consensus site (Delye, Mitra & Sept) of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on site residue Thr239 (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compounds 1, 4, 8 and reference compound trifluraline, docked to the Consensus site (Delye, Mitra & Sept) of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on site residue Thr239 (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, and reference compound trifluraline, docked to the M-loop region of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the M-loop region residue Leu286 (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-5 and 7-9, docked to the interface region between two neighboring alpha-tubulin monomers of Trypanosoma cruzi; alpha-tubulin homology models were built on PDB-ID 5ubq and two monomeric models were aligned to neighboring protofilaments of the original PDB-ID 5ubq to construct an interface-model receptor. The docking grid was centered on the M-loop region residue ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, and reference compound trifluralin, docked to the N-loop region of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the N-loop region residue Phe49 (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compounds 1, 2, 4, 8 and reference compound trifluraline, docked to the pironetin site of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on site residue Leu238 (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compounds 1-2, 4-5 and 7-8, docked to the resulting complex of reference compound trifluralin in the Blume site of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the trifluralin reference compound (T. cruzi numbering). No results were obtained for compounds 3, 6 and 9.

The docking results were obtained by Induced Fit docking ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compounds 1-5 and 7-8, docked to the resulting complex of reference compound trifluralin in the Consensus site of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the trifluralin reference compound (T. cruzi numbering). No results were obtained for compounds 6 and 9.

The docking results were obtained by Induced Fit docking ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the resulting complex of reference compound trifluralin to the M-loop region of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the trifluralin reference compound (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the resulting complex of reference compound trifluralin to the N-loop region of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the trifluralin reference compound (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for dinitroaniline etherphospholipid hybrid compounds 1-4 and 7-8 docked to the resulting complex of reference compound trifluralin in the pironetin site of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the trifluralin reference compound (T. cruzi numbering). No results were obtained for compounds 5, 6 and 9.

The docking results were obtained by Induced Fit docking with ...

Trypanosoma cruzi multimeric alpha-tubulin protein receptor for docking studies, generated by alignment of two identical models of T. cruzi alpha-tubulin on template 5ubq alpha-tubulin chains of two neighboring protofilaments (A, C).

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

Results of the statistical analysis, identifying proteins that change in abundance significantly across photoperiods.

In vitro early toxicity profiles (all experiments were performed in triplicate, IC50 in μM) for the reference drugs Pentamidine (PEN), Benzidazole (BZD), Amphotericin B (AmB) and Miltefosine (MIL).

Very simplistic unrealistic values for tamoxifen Kinetics (Km). For use in a simple graphical model.

Creator: Hannah O'Keefe

Submitter: Hannah O'Keefe

grid for ROMS

Creator: Xiangcheng Li

Submitter: Xiangcheng Li

No description specified

Creators: None

Submitter: Marta Eide

No description specified

Creator: Sebastian Curth

Submitter: Sebastian Curth

Out

Creator: Sebastian Curth

Submitter: Sebastian Curth

Measurement of oxidative stress (TBARS) assay in liver of cod caged in Kollevåg and at reference location.

Creators: None

Submitter: Karina Dale

PDB file of the prepared Trypanosoma brucei dihydrofolate reductase docking receptor based on chain A of PDB-ID 3rg9 without water molecules.

PDB file of the prepared Trypanosoma brucei pteridine reductase 1 docking receptor based on chain A of PDB-ID 2x9g with a conserved set of structural waters.

PDB file of the prepared Trypanosoma brucei pteridine reductase 1 docking receptor based on chain A of PDB-ID 2x9g without additional water molecules.

A brief summary of the first activity, proposed in our teaching sequence.

Creator: Ioannis Metaxas

Submitter: Ioannis Metaxas

A brief description of the second educational activity.

Creator: Ioannis Metaxas

Submitter: Ioannis Metaxas

A brief discription of the third educational activity.

Creator: Ioannis Metaxas

Submitter: Ioannis Metaxas

Simulation results of temperature degradation of gluconeogenic intermediates

Experimental data for determination of half-life of gluconeogenic intermediates (BPG, GAP and DHAP).

MIAPE based Gel Electrophoresis Data Entry Worksheet

columns are 'id' ,'name', 'term_type' , 'GOID', 'is_obsolete','is_root' and 'is_relation'

columns are 'id' ,'name', 'term_type' , 'GOID', 'is_obsolete','is_root' and 'is_relation'

Testing data upload

Creator: Chris Wilson

Submitter: Chris Wilson

How to connect to the FAIRDOM SEEK with the collection of their APIs.

Creators: None

Submitter: Andrej Blejec

No description specified
No description specified
No description specified

test file

Creators: Olga Krebs, Vânia Pobre

Submitter: Olga Krebs

No description specified

Creator: Birger Wolter

Submitter: Birger Wolter

Excel file with data on levels of thiamine and its metabolites TMP and active cofactor TDP, tested in Col and prr7prr9 samples from study Laurel and Hardy 3. Altered levels of TDP could potentially affect enzymes with TDP cofactors that metabolise malate and fumarate levels, altering their levels in prr7prr9.

Creators: Yin Hoon Chew, Michael Moulin, Teresa Fitzpatrick

Submitter: Andrew Millar

The fasta file contains amino acid sequences of genes forming the accessory genome of the Clostridium beijerinckii species.

Creator: Karel Sedlar

Submitter: Karel Sedlar

The fasta file contains amino acid sequences of genes forming the accessory genome of the Clostridium beijerinckii species. As BLAST might experience some errors with repetitive sequences, here 76 sequences with a single kind of amino acid forming more than 25% of a sequence were discarded.

Creator: Karel Sedlar

Submitter: Karel Sedlar

Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an ...

The fasta file contains amino acid sequences of genes forming the core genome of the Clostridium beijerinckii species.

Creator: Karel Sedlar

Submitter: Karel Sedlar

Heterologous Expression of LDHs from different lactic acid bacteria in Escherichia coli DH5α.

Assessment of kinetic parameters of LDH to include in a catabolic model.

Here published artikel about The FAIR Guiding Principles for scientific data management and stewardship

TOK1 TRK1 TRK2

Creator: Silvia Petrezselyova

Submitter: The JERM Harvester

How to get to the hotel from rail station

Creator: Olga Krebs

Submitter: Olga Krebs

It includes annotation number data at June 2012, June 2016 and Jan 2021.

Additional file 2

Westerhoff H.V. and Van Dam K. (1987) Thermodynamics and control of biological free-energy transduction, Elsevier, Amsterdam ISBN: 0-444-80783-7 (U.S.)

This monograph gives the basis of both non equilibrium thermodynamics and metabolic control analysis in biology. It is rife with examples from bioenergetics.

It is also a compilation of mathematical equations and text and hence serves as a data file for mathematical biology and biological modelling

working document 31 January 2022 Context is the equilibrium constants measurement standardization

Creators: Hans V. Westerhoff, Peter Halling

Submitter: Hans V. Westerhoff

No description specified

Creator: Huseyin Tas

Submitter: Huseyin Tas

No description specified

RNA levels for control amplicons and multiple clock genes in 2 WT (Col, Ws) and 5 clock mutants of Arabidopsis, in biological duplicates, from three conditions: Diurnal cycle (12L/12D), Extended night (DD), Extended light (LL), harvested every 2 hours. Numbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells. Comments: Data from LD are concateneted with DD and LL for better visualization. Toc1-101 (col-0) gi-201 (col-0) prr7-3 prr9-1 (col-0) , lhy cca1 (ws) elf3-4 ...

Analysis of carbon metabolites in clock mutants by Anna Flis and Ronan Sulpice, Mark Stitt lab

Creators: Andrew Millar, Anna Flis, Ronan Sulpice, Mark Stitt

Submitter: Andrew Millar

Batch sample publishing

No description specified

This pdf contains the top 10 markers for each identified cell type as a dot-plot.

This file contains the top markers for the identified cell types.

This dot-plot represents only the most significant genes per identified cell type cluster.

This pdf contains the top 10 markers for each identified cell type as a dot-plot.

This file contains the top 100 transcripts for the identified cell types in the integrated dataset.

No description specified

Kinetic characterisation of TPI. Experimental data for enzyme reaction rates with increasing concentrations of DHAP and GAP, and inhibition with 3PG and PEP.

Experimental data set for the kinetic characterisation of TPI

Simulation results of TPI experimental data for GAP and DHAP saturation.

TPM counts for protein coding genes, alongside functional annotations

Deatiled agenda forBest practices in research data management and stewardship (2021-06-14)

Creator: Olga Krebs

Submitter: Olga Krebs

No description specified

Creator: Praveen kumar Sappa

Submitter: The JERM Harvester

Mutants with defects in glucose transport systems were analyzed in a bioreactor and the transcription of certain uptake systems analyzed. Transcription profiles between batch and chemostat conditions were compared

Creator: Sonja Steinsiek

Submitter: Sonja Steinsiek

Transcription of glucose uptake transport systems in a mutant background under aerobic batch conditions.

Transcription of glucose uptake transport systems in a mutant background under anaerobic batch conditions.

Transcriptome analysis suggests a compensatory role of the cofactors coenzyme A and NAD+ in medium-chain acyl-CoA dehydrogenase knockout mice. During fasting, mitochondrial fatty-acid β-oxidation (mFAO) is essential for the generation of glucose by the liver. Children with a loss-of-function deficiency in the mFAO enzyme medium-chain acyl-Coenzyme A dehydrogenase (MCAD) are at serious risk of life-threatening low blood glucose levels during fasting in combination with intercurrent disease. However, ...

Micro array analysis of steady-state growing cells of Clostridium acetobutylicum at pH 5.7 (acidogenesis) in comparison to pH 4.5 (solventogenesis).

Micro array analyses of all mRNA levels of cells growing at steady state pH values 5.7, 5.5, 5.3, 5.1, 4.9, 4.7 compared to the same reference steady-state pH 4.5.

In this study, we used publically available dataset from gene expression omnibus (GEO):

The pathophysiological mechanisms that drive non-alcoholic fatty liver disease (NAFLD) progression remain poorly understood. This multicenter study characterized the transcriptional changes that occur as liver disease progresses. 216 snap frozen liver biopsies, comprising 206 NAFLD cases with different fibrosis stages and 10 controls were studied. Samples underwent high-throughput RNA sequencing. This study ...

Creator: Govaere O et.al.

Submitter: Hong Yang

No description specified

Creator: Angeles Hueso-Gil

Submitter: Angeles Hueso-Gil

This template is for recording gene expression data from the NimbleGen platform. This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

RNAseq analysis of S. solfataricus grown on either L-fucose or D-glucose

An example template for MAGE-TAB compliant transcriptomics data. This example only covers the Investigation Description Format (IDF) and the Sample and Data Relationship Format (SDRF) worksheets (i.e. the metadata from a microarray experiment). This template was generated automatically using the ArrayExpress submission help tool (http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi)

Please fill in thistravel expense reimbursement report and send it together with original receipts to HITS

Creator: Olga Krebs

Submitter: Olga Krebs

Data file for PLaSMo accesssion ID PLM_5, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

TRK1, TRK2

Creator: Silvia Petrezselyova

Submitter: The JERM Harvester

All datapoints that were measured are displayed together with the accompanying simulations by the computational model

The tutorial provided for EraSysAPP PALs. Covers new features associated with generating snapshots, research objects, and assigning DOIs to investigation snapshots in order to make them citable structures.

Creator: Natalie Stanford

Submitter: Natalie Stanford

Source code for running simulations

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