Disseminating structural genomics data to the public: from a data dump to an animated story

Abagyan, Ruben; Lee, Wen‐Hwa; Raush, Eugene; Budagyan, Levon; Totrov, Maxim; Sundström, M.

doi:10.1016/j.tibs.2005.12.006

Cited by 42 publications

(36 citation statements)

References 3 publications

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“…The visualization is extended to 3D by either using the simple Jmol viewer (www.jmol.org) or the rich ICM-Browser (free at www.molsoft.com). The generated data files are fully interactive and use the iSee technology (Abagyan et al, 2006).…”

Section: Methodsmentioning

confidence: 99%

DFprot: a webtool for predicting local chain deformability

et al. 2007

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Summary: DFprot is a web-based server for predicting main-chain deformability from a single protein conformation. The server automatically performs a normal-mode analysis (NMA) of the uploaded structure and calculates its capability to deform at each of its residues. Non-specialists can easily and rapidly obtain a quantitative first approximation of the flexibility of their structures with a simple and efficient interface.

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Section: Methodsmentioning

confidence: 99%

DFprot: a webtool for predicting local chain deformability

et al. 2007

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“…Finally, all the docking solutions in which the soluble electron carrier was clashing with the membrane (i.e., any Pc or Cyt atom within a distance of less than 3 Å from any lipid molecule of the membrane) were removed. Atomic distances and clashes were computed with ICMBrowser program [41] (www.molsoft.com).…”

Section: Protein-protein Docking Simulationsmentioning

confidence: 99%

Interaction of photosystem I from Phaeodactylum tricornutum with plastocyanins as compared with its native cytochrome c6: Reunion with a lost donor

Bernal‐Bayard

Pallara

Castell

et al. 2015

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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In the Phaeodactylum tricornutum alga, as in most diatoms, cytochrome c6 is the only electron donor to photosystem I, and thus they lack plastocyanin as an alternative electron carrier. We have investigated, by using laser-flash absorption spectroscopy, the electron transfer to Phaeodactylum photosystem I from plastocyanins from cyanobacteria, green algae and plants, as compared with its own cytochrome c6. Diatom photosystem I is able to effectively react with eukaryotic acidic plastocyanins, although with less efficiency than with Phaeodactylum cytochrome c6. This efficiency, however, increases in some green alga plastocyanin mutants mimicking the electrostatics of the interaction site on the diatom cytochrome. In addition, the structure of the transient electron transfer complex between cytochrome c6 and photosystem I from Phaeodactylum has been analyzed by computational docking and compared to that of green lineage and mixed systems. Taking together, the results explain why the Phaeodactylum system shows a lower efficiency than the green systems, both in the formation of the properly arranged [cytochrome c6-photosystem I] complex and in the electron transfer itself.

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“…Dissemination of this structure-mutation map in an intuitive and approachable manner is therefore essential for 'reaching-out' to a diverse clientele especially outside the structural biology field. Relevant to this, as a clear mandate to deliver data to the scientific community, the SGC has been producing 'iSEE datapacks,' which are freely available, web-based interactive documents highlighting the salient features for each of our deposited structures (Abagyan et al 2006;Lee et al 2009) (for the current list of available datapacks, visit http://www.thesgc. org/iSee/).…”

Section: From Structure To Understanding Mutationsmentioning

confidence: 99%

High‐throughput structural biology of metabolic enzymes and its impact on human diseases

Yue

Oppermann

2011

J of Inher Metab Disea

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The Structural Genomics Consortium (SGC) is a public-private partnership that aims to determine the three-dimensional structures of human proteins of medical relevance and place them into the public domain without restriction. To date, the Oxford Metabolic Enzyme Group at SGC has deposited the structures of more than 140 human metabolic enzymes from diverse protein families such as oxidoreductases, hydrolases, oxygenases and fatty acid transferases. A subset of our target proteins are involved in the inherited disorders of carbohydrate, fatty acid, amino acid and vitamin metabolism. This article will provide an overview of the structural data gathered from our high-throughput efforts and the lessons learnt in the structure-function relationship of these enzymes, small molecule development and the molecular basis of disease mutations.

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Disseminating structural genomics data to the public: from a data dump to an animated story

Cited by 42 publications

References 3 publications

DFprot: a webtool for predicting local chain deformability

DFprot: a webtool for predicting local chain deformability

Interaction of photosystem I from Phaeodactylum tricornutum with plastocyanins as compared with its native cytochrome c6: Reunion with a lost donor

High‐throughput structural biology of metabolic enzymes and its impact on human diseases

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