Dataset Information

Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf.

ABSTRACT: The ConSurf web-sever for the analysis of proteins, RNA, and DNA provides a quick and accurate estimate of the per-site evolutionary rate among homologues. The analysis reveals functionally important regions, such as catalytic and ligand-binding sites, which often evolve slowly. Since the last report in 2016, ConSurf has been improved in multiple ways. It now has a user-friendly interface that makes it easier to perform the analysis and to visualize the results. Evolutionary rates are calculated based on a set of homologous sequences, collected using hidden Markov model-based search tools, recently embedded in the pipeline. Using these, and following the removal of redundancy, ConSurf assembles a representative set of effective homologues for protein and nucleic acid queries to enable informative analysis of the evolutionary patterns. The analysis is particularly insightful when the evolutionary rates are mapped on the macromolecule structure. In this respect, the availability of AlphaFold model structures of essentially all UniProt proteins makes ConSurf particularly relevant to the research community. The UniProt ID of a query protein with an available AlphaFold model can now be used to start a calculation. Another important improvement is the Python re-implementation of the entire computational pipeline, making it easier to maintain. This Python pipeline is now available for download as a standalone version. We demonstrate some of ConSurf's key capabilities by the analysis of caveolin-1, the main protein of membrane invaginations called caveolae.

SUBMITTER: Yariv B

PROVIDER: S-EPMC9942591 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf.

Yariv Barak B Yariv Elon E Kessel Amit A Masrati Gal G Chorin Adi Ben AB Martz Eric E Mayrose Itay I Pupko Tal T Ben-Tal Nir N

Protein science : a publication of the Protein Society 20230301 3

The ConSurf web-sever for the analysis of proteins, RNA, and DNA provides a quick and accurate estimate of the per-site evolutionary rate among homologues. The analysis reveals functionally important regions, such as catalytic and ligand-binding sites, which often evolve slowly. Since the last report in 2016, ConSurf has been improved in multiple ways. It now has a user-friendly interface that makes it easier to perform the analysis and to visualize the results. Evolutionary rates are calculated ...[more]

PMID: 36718848

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Project description:BackgroundIn the United States, patients can access their electronic health record (EHR) data through patient portals. However, current patient portals are mainly focused on a single provider, with very limited data sharing capabilities and put low emphasis on independent sensemaking of the EHR data. This makes it very challenging for patients to switch between different portals and aggregate the data to obtain a complete picture of their medical history and to make sense of it. Owing to this fragmentation, patients are exposed to numerous inconveniences such as medical errors, repeated tests, and limited self-advocacy.ObjectiveTo overcome the limitations of EHR patient portals, we designed and developed Discovery-a web-based application that aggregates EHR data from multiple providers and present them to the patient for efficient exploration and sensemaking. To learn how well Discovery meets the patients' sensemaking needs and what features should such applications include, we conducted an evaluation study.MethodsWe conducted a remote study with 14 participants. In a 60-minute session and relying on the think-aloud protocol, participants were asked to complete a variety of sensemaking tasks and provide feedback upon completion. The audio materials were transcribed for analysis and the video recordings of the users' interactions with Discovery were annotated to provide additional context. These combined textual data were thematically analyzed to surface themes that reflect how participants used Discovery's features, what sensemaking of their EHR data really entails, and what features are desirable to support that process better.ResultsWe found that Discovery provided much needed features and could be used in a variety of everyday scenarios, especially for preparing and during clinical visits and also for raising awareness, reflection, and planning. According to the study participants, Discovery provided a robust set of features for supporting independent exploration and sensemaking of their EHR data: summary and quick overview of the data, finding prevalence, periodicity, co-occurrence, and pre-post of medical events, as well as comparing medical record types and subtypes across providers. In addition, we extracted important design implications from the user feedback on data exploration with multiple views and nonstandard user interface elements.ConclusionsPatient-centered sensemaking tools should have a core set of features that can be learned quickly and support common use cases for a variety of users. The patients should be able to detect time-oriented patterns of medical events and get enough context and explanation on demand in a single exploration view that feels warm and familiar and relies on patient-friendly language. However, this view should have enough plasticity to adjust to the patient's information needs as the sensemaking unfolds. Future designs should include the physicians in the patient's sensemaking process and improve the communication in clinical visits and via messaging.

Dataset Information

Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf.

Publications

Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf.

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