Digitisation projects at the University of Dundee Archive Services

Brown, Caroline

doi:10.1108/00330330610669280

Cited by 7 publications

(5 citation statements)

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“…RMSD-based heat maps were prepared to support identification of similarities in the set of predictions. OC cluster analysis program was run with the default settings (single linkage algorithm) to calculate the centroids of the 3D structure ensembles of the RNA [ 68 ].…”

Section: Methodsmentioning

confidence: 99%

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

Gumna

Antczak

Adamiak

et al. 2022

IJMS

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RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5′- and 3′-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.

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Section: Methodsmentioning

confidence: 99%

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

Gumna

Antczak

Adamiak

et al. 2022

IJMS

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“…For instance, most users prefer to have less text on screen and more icons instead [5]. Moreover, users expect to see images of materials available on OPACs [8]. In updating and introducing a new version of OPAC services, users should be comfortable with the new version and should not struggle to do their task and be able to "find what they need, when they need it and in a form they want it" [6].…”

Section: Introductionmentioning

confidence: 99%

User perceptions of online public library catalogues

Kani‐Zabihi

Ghinea

Chen

2008

International Journal of Information Management

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Online Public Library Catalogues (OPACs) are widely used electronic library catalogues giving a wealth of remote access to library information resources. Users should be involved early in the OPAC development cycle process in order to ensure a usable and functional interface, as the integration of user-defined requirements of OPACs, along with the other Human-Computer Interaction considerations, offer a better understanding of user perceptions and expectations respect of OPACs, ultimately resulting in truly user-centred OPACs. Accordingly, the purpose of this study was to establish user suggestions for a typical OPAC application's functionality and features. To this end, an experiment was undertaken to find out the type of interaction features that users prefer to have in an OPAC. The study revealed that regardless of users' Information Technology (IT) backgrounds, their functionality expectations of OPACs are the same as users are expecting OPACs to facilitate easier ways to achieve their tasks. However, based on users' previous experiences with OPACs, their requirements with respect to specific features may change.

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“…The author concludes that for such an archive to be successful, more sophisticated indexing techniques and interactions are required. This view is further supported by Brown [3], who notes that sophisticated searching functionality is required for the successful creation of a digital archive.…”

Section: Related Workmentioning

confidence: 93%