MolViewSpec: a Mol* extension for describing and sharing molecular visualizations - PubMed (original) (raw)

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations

Adam Midlik et al. Nucleic Acids Res. 2025.

Abstract

Data visualization is a pivotal component of a structural biologist's arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.

© The Author(s) 2025. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Conflict of interest statement

None declared.

Figures

Graphical Abstract

Graphical Abstract

Figure 1.

Figure 1.

Illustration of selected MolViewSpec features. (A) apo-form [PDB ID 2e2n, chain A] and the glucose-binding form [PDB ID 2e2o, chain A] of the ATP-dependent hexokinase from Sulfolobus tokodaii [18], superposed based on its the largest domain. (B) An AlphaFold predicted structure (UniProt ID Q868N5) colored by residue-wise predicted Local Distance Difference Test (pLDDT) confidence score [19]. (C) Predicted membrane orientation for the β2 adrenergic receptor–Gs protein complex (PDB ID 3sn6 [20]). (D) Electron density map around a ligand (HEM, PDB ID 1tqn [21]). See Supplementary Materials 2–5 for source code of these examples. More examples are available at

molstar.org/mol-view-spec

.

Figure 2.

Figure 2.

MolViewSpec architecture. (A) The client application requests a view from a server, (B) the server utilizes the MolViewSpec API to (C) reference and/or transform data sources and (D) generate MolViewSpec State (encoded as a JSON object), which (E) can be interpreted by a viewer; (F) the client application passes the MolViewSpec State to the viewer. Steps (B)–(D) can be replaced by serving a pre-generated static MolViewSpec State file instead of generating it dynamically.

Figure 3.

Figure 3.

Structural stories of BCR-ABL kinase and TBP. MolViewSpec can be used to create interactive storyboards. We illustrate this by showing (A) how structural changes drive disease, influence structure-based drug discovery, and contribute to drug resistance in BCR-ABL kinase (PDB ID 1opl [24]) by visualising key molecular features such as the ATP-binding pocket, regulatory domains, and drug resistance-associated mutations in the kinase catalytic domain; and (B) the critical role of the highly conserved TBP in initiating mRNA transcription in eukaryotes by highlighting protein–DNA interactions resulting in subtle conformation changes in TBP and an unprecedented distortion in DNA (structural alignment of 1cdw [23] and 1vtl [25] shown). Explore the full stories at

molstar.org/demos/mvs-stories

. The application can be embedded into 3rd party web pages and used as a template to tell similar narratives.

Figure 4.

Figure 4.

MolViewSpec-guided Mol* illustration of a multiscale integrative structure and associated distance restraints from crosslinking mass spectrometry data. The structure of the Nup84 subcomplex of the Nuclear Pore Complex from budding yeast obtained from an integrative modeling [28] is shown. The structure is archived in the PDB-IHM sub-directory of the PDB (PDB ID 8zz1) and is based on input restraints from crosslinking-MS data and 2D electron microscopy class averages. The coarse-grained spherical beads at different granularities in the multiscale model are depicted. Individual subunits in the Nup84 subcomplex are identified using different colors and labels. The intra- and inter-subunit crosslink restraints used in the model are identified using dotted lines with an example crosslink highlighted and available as a tooltip. An interactive version is available at

molstar.org/demos/ihm-restraints

.

References

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