The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations

Abstract

We present the Biological Structure Model Archive (BSM-Arc, https://bsma.pdbj.org), which aims to collect raw data obtained via in silico methods related to structural biology, such as computationally modeled 3D structures and molecular dynamics trajectories. Since BSM-Arc does not enforce a specific data format for the raw data, depositors are free to upload their data without any prior conversion. Besides uploading raw data, BSM-Arc enables depositors to annotate their data with additional explanations and figures. Furthermore, via our WebGL-based molecular viewer Molmil, it is possible to recreate 3D scenes as shown in the corresponding scientific article in an interactive manner. To submit a new entry, depositors require an ORCID ID to login, and to finally publish the data, an accompanying peer-reviewed paper describing the work must be associated with the entry. Submitting their data enables researchers to not only have an external backup but also provide an opportunity to promote their work via an interactive platform and to provide third-party researchers access to their raw data.

Keywords: Archive; Database; Homology modeling; Molecular dynamics; Raw data; Sharing.

Fig. 1

Editor/submission tool showing BSM-00001. The top-center panel (named “Project editor”) can be used to add meta-data to the entry and add extensive descriptions via full-text panels. The bottom-center panel (named “File manager”) can be used to upload new files (either via drag-and-drop operations or via the buttons) and assign per-file/folder annotations (description). Double clicking on supported files opens them in the BSM-Arc viewer (e.g., the file fig1B.mjs is shown in the bottom-right corner), while double clicking on folders accesses the clicked folder. Right clicking shows a context menu from which, e.g., the description can be modified and the files downloaded

Fig. 2

List of published entries at https://bsma.pdbj.org/search/bsma. Published entries are shown as their title, the authors, a graphical abstract set by the depositors, and the deposition, modification, and release dates

Fig. 3

Published entry BSM-00001 at https://bsma.pdbj.org/entry/1. a In the top panel, the title, graphical abstract, authors, DOI, and links to external databases are listed. Below that, the free-text panels configured by the depositors are shown and finally the file manager, which works as the file manager described in Fig. 1, except no files can be uploaded and no modifications can be made. Here, two methods of annotation are used, first via a free-text panel (named “Description”), which describes the general layout of the uploaded data. Secondly, for the major files and folders, a per-file or per-folder description is included in the “File manager” panel. b List of raw data files included in one of the raw data folders of the entry (https://bsma.pdbj.org/entry/1/path/data/raw/300K/1fvc/1). The input and output files (both ASCII and binary) to/from the MD software were uploaded as is, without any modifications. For this entry, the individual trajectory files (md.xtc) were outputted during the simulation without solvent, making the trajectory files relatively small (albeit that there are 250 such trajectories in this entry). c The file md.gro loaded using the integrated Molmil viewer. In order to load a trajectory file (e.g., md.xtc) from this state, Molmil’s command line must be used, which can be accessed by clicking on the “<” icon in the bottom-left corner. From here, entering the command “load md.xtc” will download and load the file. Finally, to play the trajectory, the “mplay” command can be used