Dataset Information

Fully automated antibody structure prediction using BIOVIA tools: Validation study.

ABSTRACT: We describe the methodology and results from our validation study of the fully automated antibody structure prediction tool available in the BIOVIA (formerly Accelrys) protein modeling suite. Extending our previous study, we have validated the automated approach using a larger and more diverse data set (157 unique antibody Fv domains versus 11 in the previous study). In the current study, we explore the effect of varying several parameter settings in order to better understand their influence on the resulting model quality. Specifically, we investigated the dependence on different methods of framework model construction, antibody numbering schemes (Chothia, IMGT, Honegger and Kabat), the influence of compatibility of loop templates using canonical type filtering, wider exploration of model solution space, and others. Our results show that our recently introduced Top5 framework modeling method results in a small but significant improvement in model quality whereas the effect of other parameters is not significant. Our analysis provides improved guidelines of best practices for using our protocol to build antibody structures. We also identify some limitations of the current computational model which will enhance proper evaluation of model quality by users and suggests possible future enhancements.

SUBMITTER: Kemmish H

PROVIDER: S-EPMC5436848 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Fully automated antibody structure prediction using BIOVIA tools: Validation study.

Kemmish Helen H Fasnacht Marc M Yan Lisa L

PloS one 20170518 5

We describe the methodology and results from our validation study of the fully automated antibody structure prediction tool available in the BIOVIA (formerly Accelrys) protein modeling suite. Extending our previous study, we have validated the automated approach using a larger and more diverse data set (157 unique antibody Fv domains versus 11 in the previous study). In the current study, we explore the effect of varying several parameter settings in order to better understand their influence on ...[more]

PMID: 28542300

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Project description:BackgroundAssessment of food intake is a cornerstone of nutritional research. However, the use of minimally validated dietary assessment methods is common and can generate misleading results. Thus, there is a need for valid, precise and cost-effective dietary assessment tools to be used in large cohort studies.The objective is to validate a newly developed automated self-administered web-based 24-h dietary recall (R24W), within a population of adults taking part in fully controlled feeding studies.MethodsSixty two adults completed the R24W twice while being fed by our research team. Actual intakes were precisely known, thereby allowing the analysis of the proportion of adequately self-reported items. Association between offered and reported portion sizes was assessed with correlation coefficients and agreement with the kappa score while systematics biases were illustrated with Bland-Altman Plot.ResultsParticipants received an average of 16 food items per testing day. They reported 89.3% of the items they received. The more frequently omitted food categories were vegetables included in recipes (40.0%) as well as side vegetables (20.0%) and represented less than 5% of the actual daily energy intake. Offered and self-reported portion sizes were significantly correlated (r = 0.80 P < 0.001) and demonstrated a strong agreement as assessed by the kappa score of 0.62. Reported portion sizes for individual food items were on average 3.2 g over the offered portion sizes. Portions of 100 g and above were on average underestimated by 2.4% (r = 0.68 P < 0.01; kappa score = 0.50) while small portions (less than 100 g) were overestimated by 17.1% (r = 0.46 P < 0.01; kappa score = 0.43). A nonsignificant underestimation (-13.9 kcal ± 646.3 kcal; P = 0.83) of energy intake was noted.ConclusionR24W performed well as participants were able to report the great majority of items they ate and selected portion size strongly related to the one they received. This suggests that food items are easily to find within the R24W and images of portion sizes used in this dietary assessment tool are adequate and can provide valid food intake evaluation.

Dataset Information

Fully automated antibody structure prediction using BIOVIA tools: Validation study.

Publications

Fully automated antibody structure prediction using BIOVIA tools: Validation study.

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