Dataset Information

Rapid generation of high-quality structure figures for publication with PyMOL-PUB.

ABSTRACT:

Motivation

The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and/or program call commands. Therefore, providing interfaces based on established software instead of manual editing becomes a significant necessity.

Results

We developed PyMOL-PUB, based on the original design of PyMOL, to effectively create publication-quality figures from molecular structure data. It provides functions including structural alignment methods, functional coloring schemes, conformation adjustments, and layout plotting strategies. These functions allow users to easily generate high-quality figures, demonstrate structural differences, illustrate inter-molecular interactions, and predict performances of biomacromolecules.

Availability and implementation

Our tool is publicly available at https://github.com/BGI-SynBio/PyMOL-PUB.

SUBMITTER: Chen Y

PROVIDER: S-EPMC10950480 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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Publications

Rapid generation of high-quality structure figures for publication with PyMOL-PUB.

Chen Yuting Y Zhang Haoling H Wang Wen W Shen Yue Y Ping Zhi Z

Bioinformatics (Oxford, England) 20240301 3

<h4>Motivation</h4>The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and/o ...[more]

PMID: 38449297

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Project description:Background. The need for timely, ethical, and high-quality reporting of clinical trial results has seen a rise in demand for publication professionals. These publication experts, who are not ghostwriters, work with leading medical researchers and funders around the world to plan and prepare thousands of publications each year. Despite the involvement of publication professionals in an increasing number of peer-reviewed publications, especially those that affect patient care, there is limited evidence-based guidance in the peer-reviewed literature on their publication practices. Similar to the push for editors and the peer-review community to conduct and publish research on publication ethics and the peer-review process, the International Society for Medical Publication Professionals (ISMPP) has encouraged members to conduct and publish research on publication planning and practices. Our primary objective was to investigate the publication rate of research presented at ISMPP Annual Meetings. Methods. ISMPP Annual Meeting abstract lists (April 2009-April 2014) were searched in November 2014 and data were extracted into a pilot-tested spreadsheet. MEDLINE was searched in December 2014 to determine the publication rate (calculated as the % of presented abstracts published as full papers in peer-reviewed journals). Data were analyzed using the Cochran-Armitage trend test (significance: P < .05) by an independent academic statistician. Results. From 2009 to 2014, there were 220 abstracts submitted, 185 accepted, and 164 presented. There were four corresponding publications (publication rate 2.4%). Over time, ISMPP's abstract acceptance rate (overall: 84.1%) did not change, but the number of abstracts presented increased significantly (P = .02). Most abstracts were presented as posters (81.1%) and most research was observational (72.6%). Most researchers came from the US (78.0%), followed by Europe (17.7%), and the Asia-Pacific region (11.2%). Discussion. Research presented at ISMPP Annual Meetings has rarely been published in peer-reviewed journals. The high rate of nonpublication by publication professionals has now been quantified and is of concern. Publication professionals should do more to contribute to evidence-based publication practices, including, and especially, their own. Unless the barriers to publication are identified and addressed, the practices of publication professionals, which affect thousands of peer-reviewed publications each year, will remain hidden and unproven.

Dataset Information

Rapid generation of high-quality structure figures for publication with PyMOL-PUB.

Motivation

Results

Availability and implementation

Publications

Rapid generation of high-quality structure figures for publication with PyMOL-PUB.

Similar Datasets

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