3D molecular models
About 3D molecular models
Authors of selected Elsevier journals are invited to enrich their online articles by providing supplementary 3D molecular models, which will be visualized using the interactive 3D viewer embedded within the article.
Using the 3D molecular viewer, the reader can browse through 3D models, zoom into each model, rotate and pan the model, change display settings, and download original data files. It is also possible to open the 3D viewer in a new window.
The viewer has been developed in collaboration with Kitware SAS.
Representation of how the 3D models will appear on ScienceDirect
Benefits for authors and readers
The 3D molecular models functionality enables authors to enrich and extend their articles by adding a possibility to interactively explore 3D molecular structures. This provides a way to highlight their findings in a visual and easily accessible manner, helping readers to quickly understand the relevance of a research paper, to visualize research data for deeper insights, and to access the underlying data.
Innovating & enriching content
For almost 350 years, academic articles have been published in a similar layout – a format which starts with an abstract and ends with a conclusion and a list of references. Articles were presented in this way with the reader of the printed version in mind. However most researchers now access articles online, which means that readership styles and how information is gathered have changed.
We are adapting to these changes because we want to help authors to improve how their research is presented online and readers to gain deeper insights faster. Offering the 3D molecular models functionality in our journals is just one of the ways we are doing this.
The 3D molecular models functionality enables authors to enrich and extend their articles by providing a possibility to interactively explore 3D molecular structures and hence make their underlying data better accessible. This helps readers to quickly understand the relevance of a research paper and to visualize research data for deeper insights.
Supported data formats
The Elsevier’s 3D molecular viewer supports the following data formats: PDB, PSE, MOL and MOL2.
PDB is the Protein Data Bank file format. It is a textual file format describing three dimensional structures of molecules held in the RCSB Protein Data Bank (PDB). The format specification can be found here.
PSE (PyMOL Session file format) is a dictionary representation of a PyMOL session. A session is one particular conformation of a molecule (color scheme, camera, lighting effects, etc.).This format is very specific and requires the application: PyMOL to be used.
MOL (also called MDL) is a file format created by MDL for holding information about the atoms, bonds, connectivity and coordinates of a molecule. The format specification can be found here.
MOL2 isa Tripos Mol2 file. It is a complete, portable representation of a SYBYL molecule. The format specification can be found here.
The following tools can be used to prepare/export 3D molecular models in/to the aforementioned data formats: PyMOL, RasMol, MolView, YASARA, QuteMol, Coot, UCSF Chimera, etc.
Submission & publication
Each 3D molecular model should be uploaded to EES separately via the “3D molecular models” submission category. The 3D molecular data should support the following formats: PDB (.pdb), PSE (.pse), MOL (.mol)and MOL2 (.mol2). Molecular data submitted in other formats will not be processed.
3D molecular structures will be provided in the online version of the article. The PDF/printed version of the article will feature static figures only (if those figures are included in the article manuscript). In the online version, it will also be possible to download the original data files.
If you wish to provide feedback on the 3D molecular models or have a suggestion for another innovation that would further enhance the online article please get in touch.
