Integrative modelling

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CHEBI ID

CHEBI:16027 (24)
CHEBI:17754 (24)
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CHEBI:16001 (22)
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Metabolite Name

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First Public Date

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2019 (4)
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2020 (2)
2016 (1)
2014 (1)

Modelling Approach

Ordinary differential equation model (35)
Constraint-based model (3)

Lab affiliation

Biochemistry & Molecular Biology Cumming School of Medicine University of Calgary, Canada (2)
MRC Centre for Drug Safety Science, Department of Pharmacology & Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK. (1)
Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany (1)
Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK (1)
Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Victoria, Australia La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia (1)
Univeristy of Queensland (1)
Professor, Dept. of Biochemistry & Molecular Biology Robson DNA Science Centre, Arnie Charbonneau Cancer Institute Cumming School of Medicine, University of Calgary, Calgary, Alberta http://structurems.ucalgary.ca (1)
Histon Modifications Group BioMedical Center Ludwig-Maximilians-Universität Großhadernerstr. 9 82152 Planegg-Martinsried Tel: +49 89 2180 75775 (1)
Proteome Center Rostock, University of Rostock, Germany (1)
Children's Medical Research Insitute, The University of Sydney (1)
Distinguished Faculty Professor Utrecht University Scientific Director Netherlands Proteomics Centre and Scientific Director Utrecht Institute for Pharmaceutical Sciences Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherlands (1)
ETH Zurich, Institute of Molecular Systems Biology (1)
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India. (1)
Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, 5000, Nova Gorica, Slovenia (1)
Proteomics and Mass Spectrometry of Biomolecules, ProteoToul Research Proteomics Facility of Toulouse, ProteoToul Services Proteomics French Infrastructure, ProFI IPBS, CNRS, UMR 5089 205 route de Narbonne BP 64182 31077 Toulouse Cedex France (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands (1)
The Institute of Cancer Research (1)

IsPrivate

False (39)

Submitter Keywords

FROG (1)

Modification

2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)

Study type

Transcription profiling by array (10)
ChIP-seq (2)
Methylation profiling by array (2)
RNA-seq of total RNA (2)
RNA-seq of coding RNA (2)
Transcription profiling by tiling array (1)
Other (1)
DNA-seq (1)

Release Date

2022 (100)
2025 (84)
2021 (74)
2019 (70)
2020 (70)
2023 (64)
2024 (60)
2017 (52)
2018 (48)
2016 (46)
2015 (38)
2014 (30)
2013 (19)
2011 (14)
2010 (11)
2012 (9)
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2006 (5)
2008 (4)
2009 (3)
2005 (2)
2007 (1)

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Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection

The metabolic effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on human blood plasma were characterized using multi-platform metabolic phenotyping with Nuclear Magnetic Resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). Quantitative mea...

2021-01-29 | MTBLS2014 | MetaboLights

Integrative Threading of the DNA-PKcs Disordered Region with Crosslinking Restraints

Integrative structure modelling was applied to understand how auto-phosphorylation of the ABCDE cluster in DNA-PKcs can occur. We used crosslinking restraints to assign sequence to structurally unassigned helices in DNA-PKcs s in the largely disordered region containing the ABCDE cluster. Our final ...

ORGANISM(S): Homo sapiens (Human)

2019-12-10 | PXD016639 | Pride

Cross-linking mass spectrometry and integrative modelling of Methanocaldococcus jannaschii GMP synthetase

GMP synthetases are enzymes that catalyze the conversion of XMP to GMP. The two-subunit type GMP synthetases are composed of a glutamine amidotransferase (GATase) subunit that catalyzes the conversion of Gln to Glu and ammonia, and the ATP pyrophosphatase (ATPPase) subunit that catalyzes the formati...

ORGANISM(S): Methanocaldococcus jannaschii DSM 2661

2022-09-02 | PXD031519 | Pride

Gmp synthetase Ammonia tunnelling Cross-linking mass spectrometry Integrative modelling Allostery

Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies.

Not available

S-EPMC9035671 | biostudies-literature

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modelling

PRJNA509222 | ENA

IMProv: A Resource for Crosslink-Driven Structure Modeling that Accommodates Protein Dynamics

Crosslinking and hydrogren-deuterium exchange data of Polycomb Repressive Complex 2 used for integrative modelling.

ORGANISM(S): Homo sapiens (Human)

2021-10-12 | PXD022861 | Pride

Crosslinking mass spectrometry Software Integrative modelling

VineColD: an integrative database for global historical tracing and real-time monitoring of grapevine cold hardiness.

Not available

S-EPMC12475903 | biostudies-literature

Transcriptome-driven constraint-based modelling reveals metabolic targets for ovarian cancer

OV56 ovarian cancer cell line treated with siTPI1 (siRNA targeted against triose phosphate isomerase 1) and the following negative controls: NTsiRNA (non-targeting siRNA), transfection reagent only and untreated. Experiment designed to assess the effect of TPI1 gene knockdown on OV56 gene expression...

ORGANISM(S): Homo sapiens

2026-04-09 | E-MTAB-16770 | biostudies-arrayexpress

BioModelKit - An Integrative Framework for Multi-Scale Biomodel-Engineering.

Not available

S-EPMC6340123 | biostudies-literature

Achieving Chemical Accuracy in Cyclodextrin Host-Guest Binding via Integrative Atomistic Modelling.

Not available

S-EPMC12915143 | biostudies-literature

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