DNA Database

Jordan, Elizabeth; Carrico, Christine K.

doi:10.1126/science.7123223

Cited by 6 publications

(3 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Ever since the conception of the Protein Data Bank (PDB) , and Genbank, , open access to standardized and searchable pools of experimental data has revolutionized scientific research. Constantly growing and improving in fidelity due to collaborative effort, − the now hundreds of databanks fuel the data-driven development of biomolecular structure determination, refinement, prediction, and design approaches as well as the development of drugs, , materials, , and more. , It is clear that open data enables scientific progress that is far beyond the resources of a single research group or institute.…”

Section: Introductionmentioning

confidence: 99%

Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics

Antila

Ferreira

Ollila

et al. 2021

J. Chem. Inf. Model.

View full text Add to dashboard Cite

Molecular dynamics (MD) simulations are widely used to monitor time-resolved motions of biomacromolecules, although it often remains unknown how closely the conformational dynamics correspond to those occurring in real life. Here, we used a large set of open-access MD trajectories of phosphatidylcholine (PC) lipid bilayers to benchmark the conformational dynamics in several contemporary MD models (force fields) against nuclear magnetic resonance (NMR) data available in the literature: effective correlation times and spin–lattice relaxation rates. We found none of the tested MD models to fully reproduce the conformational dynamics. That said, the dynamics in CHARMM36 and Slipids are more realistic than in the Amber Lipid14, OPLS-based MacRog, and GROMOS-based Berger force fields, whose sampling of the glycerol backbone conformations is too slow. The performance of CHARMM36 persists when cholesterol is added to the bilayer, and when the hydration level is reduced. However, for conformational dynamics of the PC headgroup, both with and without cholesterol, Slipids provides the most realistic description because CHARMM36 overestimates the relative weight of ∼1 ns processes in the headgroup dynamics. We stress that not a single new simulation was run for the present work. This demonstrates the worth of open-access MD trajectory databanks for the indispensable step of any serious MD study: benchmarking the available force fields. We believe this proof of principle will inspire other novel applications of MD trajectory databanks and thus aid in developing biomolecular MD simulations into a true computational microscope—not only for lipid membranes but for all biomacromolecular systems.

show abstract

Section: Introductionmentioning

confidence: 99%

Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics

Antila

Ferreira

Ollila

et al. 2021

J. Chem. Inf. Model.

View full text Add to dashboard Cite

show abstract

“…Prostatic cancer was chosen as one of the human cancers analyzed in this report because of its steep agemortality curve: mortality is proportional to the 12th power of age [1], It is therefore not surprising that a recent letter [4] makes the point that 'cancer is inevit able in most people... For example, as many as 80 to 90 percent of men who live long enough develop cancer of the prostate [9]... Most people will develop cancer if they live long enough.'…”

Section: Discussionmentioning

confidence: 99%

Susceptibility to Cancer and Spontaneous Incidence

Reif¹

1983

Oncology

View full text Add to dashboard Cite

Susceptibility to cancer implies being easily affected by carcinogens, as well as having an overt spontaneous incidence of cancer. The susceptibility of a population to the development of fatal cancer of a given organ can be represented by a frequency distribution. This distribution depends both upon the genetic susceptibility of the population and upon all environmental carcinogens that have impinged on that population. The method for construction of such a susceptibility distribution has been simplified and applied to experimental data on bone tumor induction with 90Sr in mice, and to bone tumor mortality and prostate cancer mortality in man. The relative susceptibilities of different human organs to the development of fatal tumors can be defined in terms of the spontaneous tumor mortalities.

show abstract

“…The FASTA file format is widely used in genomic analysis as the repository of reference genome sequence information. FASTA was developed in 1985 (4) and is still widely used for reference genomes, but during that time the genomics ecosystem has changed dramatically; the first journal mention of a centralised DNA repository was in Elke Jordan and Christine Carrico’s Science Letter in 1982 (5). The FASTA format specification (originally the “Pearson format”) was created by William Pearson and David Lipman in 1985 (4), but has since been maintained by the National Center for Biotechnology Information (NCBI) at the U.S. National Institutes of Health (4).…”

Section: Introductionmentioning

confidence: 99%

FAIR Header Reference genome: A TRUSTworthy standard

Wright,

Wilkinson,

Mungall

et al. 2023

Preprint

View full text Add to dashboard Cite

The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability, and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability, and Technology (TRUST). The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility, and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.

show abstract

DNA Database

Cited by 6 publications

References 0 publications

Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics

Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics

Susceptibility to Cancer and Spontaneous Incidence

FAIR Header Reference genome: A TRUSTworthy standard

Contact Info

Product

Resources

About