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Evaluation of free modeling targets in CASP11 and ROLL.

ABSTRACT: We present an assessment of 'template-free modeling' (FM) in CASP11and ROLL. Community-wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-residue target (T0806-D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837-D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment-based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites. Proteins 2016; 84(Suppl 1):51-66. © 2015 Wiley Periodicals, Inc.

SUBMITTER: Kinch LN

PROVIDER: S-EPMC5576440 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

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Evaluation of free modeling targets in CASP11 and ROLL.

Kinch Lisa N LN Li Wenlin W Monastyrskyy Bohdan B Kryshtafovych Andriy A Grishin Nick V NV

Proteins 20160120

We present an assessment of 'template-free modeling' (FM) in CASP11and ROLL. Community-wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-residue target (T0806-D1) that lacked sequence similarity to any existing template. The top ...[more]

PMID: 26677002

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Project description:BackgroundThe UK was the first country to launch a national pandemic COVID-19 vaccination programme, which was implemented swiftly despite significant vaccine supply constraints. The delivery strategy used a combination of mass vaccination sites operated by NHS secondary care providers and local sites led by Primary Care Networks, and local pharmacies. Despite nation-wide rollout, persistent gaps in coverage continued to affect particular populations, including ethnic minority and marginalised social groups.AimThe study examined sub-national immunisation commissioners and providers' perspectives on how the COVID-19 vaccine programme was operationalised, and how delivery strategies impacted inequalities in access to vaccination services and uptake. The study aimed to inform national programme implementation, sustainability and future pandemic preparedness.MethodsQualitative research was conducted in eight local NHS areas in 4 regions of England. Semi-structured interviews were performed with 82 sub-national NHS and public health vaccine providers and commissioners.ResultsEngland's COVID-19 vaccination programme was described as top down, centralised and highly political. The programme gradually morphed from a predominantly mass vaccination strategy into more locally driven and tailored approaches able to respond more effectively to inequalities in uptake. Over time more flexibility was introduced, as providers adapted services by "working around" the national systems for vaccine supply and appointment booking. The constant change faced by providers and commissioners was mitigated by high staff motivation and resilience, local collaboration and pragmatism. Opportunities for efficient implementation were missed because priority was given to achieving national performance targets at the expense of a more flexible sub-national tailored delivery.ConclusionPandemic vaccination delivery models need to be adapted for underserved and hesitant groups, working in collaboration with local actors. Learnings from the initial COVID-19 vaccine roll-out in England and elsewhere is important to inform future pandemic responses, in tailoring strategies to local communities, and improve large-scale vaccination programmes.

Dataset Information

Evaluation of free modeling targets in CASP11 and ROLL.

Publications

Evaluation of free modeling targets in CASP11 and ROLL.

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