Data to knowledge: how to get meaning from your result

Berman, Helen M.; Gabanyi, Margaret; Groom, Colin R.; Johnson, John E.; Murshudov, Garib N.; Nicholls, Robert A.; Reddy, Vijay; Schwede, Torsten; Zimmerman, Matthew D.; Westbrook, John D.; Minor, Władek

doi:10.1107/s2052252514023306

Cited by 13 publications

(14 citation statements)

References 88 publications

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“…Automatic links in software used during structure determination (Dolomanov et al, 2009), the ease with which structures can be deposited, attribution of credit in the form of a DOI and continued demonstration of the value to science of depositing crystal structures (Berman et al, 2015) may help close this gap.…”

Section: Futurementioning

confidence: 99%

The Cambridge Structural Database

Groom

Bruno

Lightfoot

et al. 2016

Acta Crystallogr B Struct Sci Cryst Eng Mater

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The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

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Section: Futurementioning

confidence: 99%

The Cambridge Structural Database

Groom

Bruno

Lightfoot

et al. 2016

Acta Crystallogr B Struct Sci Cryst Eng Mater

Self Cite

8,345

214

5,026

View full text Add to dashboard Cite

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“…The protein structure was downloaded from the RCSB Protein Data Bank (http://www.rcsb.org/pdb/home/home.do) (PDB codes: 4WAF (PI3K α ), 4FJZ (PI3K γ ), and 6G6 W (PI3 K δ )). The intermolecular interactions were analyzed using PyMOL 1.7.6 (http://www.pymol.org/) . Computer simulations were used as the PI3 K β protein was not found in the RCSB Protein Data Bank.…”

Section: Methodsmentioning

confidence: 99%

“…The intermolecular interactions were analyzed using PyMOL 1.7.6 (http://www.pymol.org/). [39] Computer simulations were used as the PI3 Kβ protein was not found in the RCSB Protein Data Bank.…”

Section: Molecular Dockingmentioning

confidence: 99%

BF12, a Novel Benzofuran, Exhibits Antitumor Activity by Inhibiting Microtubules and the PI3K/Akt/mTOR Signaling Pathway in Human Cervical Cancer Cells

Gao

Feng

et al. 2020

Chemistry & Biodiversity

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BF12 [(2E)‐3‐[6‐Methoxy‐2‐(3,4,5‐trimethoxybenzoyl)‐1‐benzofuran‐5‐yl]prop‐2‐enoic acid], a novel derivative of combretastatin A‐4 (CA‐4), was previously found to inhibit tumor cell lines, with a particularly strong inhibitory effect on cervical cancer cells. In this study, we investigated the microtubule polymerization effects and apoptosis signaling mechanism of BF12. BF12 showed a potent efficiency against cervical cancer cells, SiHa and HeLa, with IC50 values of 1.10 and 1.06 μm, respectively. The cellular mechanism studies revealed that BF12 induced G2/M phase arrest and apoptosis in SiHa and HeLa cells, which were associated with alterations in the expression of the cell G2/M cycle checkpoint‐related proteins (cyclin B1 and cdc2) and alterations in the levels of apoptosis‐related proteins (P53, caspase‐3, Bcl‐2, and Bax) of these cells, respectively. Western blot analysis showed that BF12 inhibited the PI3 K/Akt/mTOR signaling pathway and induced apoptosis in human cervical cancer cells. BF12 was identified as a tubulin polymerization inhibitor, evidenced by the effective inhibition of tubulin polymerization and heavily disrupted microtubule networks in living SiHa and HeLa cells. By inhibiting the PI3 K/Akt/mTOR signaling pathway and inducing apoptosis in human cervical cancer cells, BF12 shows promise for use as a microtubule inhibitor.

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“…Oncoproteomics is rapidly changing from a discipline that originally dealt with relatively small datasets to a research area impacted by huge datasets: the era of Big Data [70]. Bioinformatics is an integral, and increasingly important, part of oncoproteomics research.…”

Section: Bioinformaticsmentioning

confidence: 99%

Oncoproteomics: Trials and tribulations

Zhou

Wang

et al. 2015

Proteomics Clinical Apps

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Oncoproteomics is the study of cancer-associated proteins and their interactions using proteomic technologies. It is expected to play a crucial role in the detection and surveillance of cancer, as well as in the development of personalized medicine for oncology. In this review, we will outline the current status, advantages, and limitations of oncoproteomics. Further, we will discuss available strategies arising from a better understanding of oncoproteomics, including integrated omics approaches, to overcome current problems in the discovery and validation of biomarkers, identification of novel drug targets, and management of personalized medicine.

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Data to knowledge: how to get meaning from your result

Cited by 13 publications

References 88 publications

The Cambridge Structural Database

The Cambridge Structural Database

BF12, a Novel Benzofuran, Exhibits Antitumor Activity by Inhibiting Microtubules and the PI3K/Akt/mTOR Signaling Pathway in Human Cervical Cancer Cells

Oncoproteomics: Trials and tribulations

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