Announcing the worldwide Protein Data Bank

Berman, Helen M.; Henrick, Kim; Nakamura, Haruki

doi:10.1038/nsb1203-980

Cited by 2,635 publications

(2,134 citation statements)

References 3 publications

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“…The RCSB PDB collaborated with data centers formed in Europe at the European Bioinformatics Institute (EMBL-EBI) and in Japan at Osaka University. In 2003, the Worldwide Protein Data Bank (wwPDB) was formed, uniting these centers to ensure that the PDB would remain a global, publicly available, and uniform archive [16,17]. The wwPDB partners (RCSB PDB [15]; Protein Data Bank in Europe, PDBe [18]; Protein Data Bank Japan, PDBj [19]) developed clear guidelines and policies for data deposition and annotation.…”

Section: Evolution Of the Protein Data Bankmentioning

confidence: 99%

The Protein Data Bank archive as an open data resource

Berman

Kleywegt

Nakamura

et al. 2014

J Comput Aided Mol Des

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117

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Section: Evolution Of the Protein Data Bankmentioning

confidence: 99%

The Protein Data Bank archive as an open data resource

Berman

Kleywegt

Nakamura

et al. 2014

J Comput Aided Mol Des

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117

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“…The simplest chiral adsorbate we studied is the amino acid tryptophan, which binds to the surface in a flat geometry via its carboxylate group and ring system, forming a planar "2-D" chiral monolayer 16 . We also studied six proteins: myoglobin, haemoglobin and bovine serum albumin, which have high levels of -helical secondary structure 18 , and -lactoglobulin, outer membrane protein A (Omp A) and concanavalin A, which have high levels of -sheet secondary structure 17 . Upon adsorption, protein tertiary structure is strongly modified by the drive to mimise the surface free energy of the interface, but secondary structure remains largely native 18 .…”

mentioning

confidence: 99%

Ultrasensitive detection and characterization of biomolecules using superchiral fields

et al. 2010

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The spectroscopic analysis of large biomolecules is important in applications such as biomedical diagnostics and pathogen detection 1,2 , and spectroscopic techniques can detect such molecules at the nanogram level or lower. However, spectroscopic techniques have not been able to probe the structure of large biomolecules with similar levels of sensitivity. Here we show that superchiral electromagnetic fields 3 , generated by the optical excitation of plasmonic planar chiral metamaterials 4,5 , are highly sensitive probes of chiral supramolecular structure. The differences in the effective refractive indices of chiral samples exposed to left-and right-handed superchiral fields are found to be up to 10 6 times greater than that those observed in optical polarimetry measurements, thus allowing picogram quantities of adsorbed molecules to be characterised. The largest differences are observed for biomolecules that possess chiral planar 2 sheets, such as proteins with high β-sheet content, which suggest that this approach could form the basis for assaying technologies capable of detecting amyloid diseases and certain types of viruses.Since the building blocks of life are chiral molecular units such as amino acids and sugars, biomacromolecules formed from these units also exhibit chirality on molecular and supramolecular scales. Chirally sensitive (chiroptical) spectroscopic techniques, such as circular dichroism (CD), optical rotatory dispersion (ORD) and Raman optical activity (ROA), are therefore especially incisive probes of the threedimensional aspects of biomacromolecular structure and are widely used in biomolecular science 1,2 . Chiroptical methods typically measure small differences, or dissymmetries, in the interaction of left-and right-circularly polarised light, the chiral probe, with a chiral material 2 . However, the inherent weakness of these existing chiroptical phenomena usually restricts their application to samples of microgram level. Recently, Tang and Cohen 3 postulated that under certain circumstances superchiral electromagnetic fields could be produced that display greater chiral asymmetry than circularly polarised plane light waves. We have realised such superchiral electromagnetic fields are generated in the near fields of PCMs, and can greatly enhanced the sensitivity of a chiroptical measurement, enabling us to detect and characterise just a few picograms of a chiral material.PCMs were first fabricated, and shown to display large chiroptical effects such as optical rotation, by Schwanecke and co-workers 4 and Gonokami and co-workers 5 .The PCMs used in this study, Fig. 1 (a), are composed of left or right handed (LH / RH) Au gammadions, of length 400 nm and thickness 100 nm (plus a 5 nm Cr adhesion layer) deposited on a glass substrate and arranged in a square lattice with a periodicity of 800 nm. As a control we repeated all experiments using a metamaterial composed of achiral crosses with the same thickness and periodicity as the gammadions: these structures showed no dissymmetry in excita...

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“…Notably, the Worldwide Protein Databank (which grew out of the Protein Databank, established in 1971 at Brookhaven National Laboratory), is an international resource to archive and disseminate biomolecular structure data (Berman et al 2003). Similarly, public repositories exist for gene sequence data (e.g.…”

Section: Initiative 3: Establishment Of a Repository Of Experimentalmentioning

confidence: 99%

Cardiac cell modelling: Observations from the heart of the cardiac physiome project

Fink

Niederer

Cherry

et al. 2011

Progress in Biophysics and Molecular Biology

146

136

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In this manuscript we review the state of cardiac cell modelling in the context of international initiatives such as the IUPS Physiome and Virtual Physiological Human Projects, which aim to integrate computational models across scales and physics. In particular we focus on the relationship between experimental data and model parameterisation across a range of model types and cellular physiological systems. Finally, in the context of parameter identification and model reuse within the Cardiac Physiome, we suggest some future priority areas for this field.

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Announcing the worldwide Protein Data Bank

Cited by 2,635 publications

References 3 publications

The Protein Data Bank archive as an open data resource

The Protein Data Bank archive as an open data resource

Ultrasensitive detection and characterization of biomolecules using superchiral fields

Cardiac cell modelling: Observations from the heart of the cardiac physiome project

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