The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
YASARA View—molecular graphics for all devices—from smartphones to workstations
Open accessAbstract
Summary: Today's graphics processing units (GPUs) compose the scene from individual triangles. As about 320 triangles are needed to approximate a single sphere—an atom—in a convincing way, visualizing larger proteins with atomic details requires tens of millions of triangles, far too many for smooth interactive frame rates. We describe a new approach to solve this ‘molecular graphics problem’, which shares the work between GPU and multiple CPU cores, generates high-quality results with perfectly round spheres, shadows and ambient lighting and requires only OpenGL 1.0 functionality, without any pixel shader Z -buffer access (a feature which is missing in most mobile devices). Availability and implementation: YASARA View, a molecular modeling program built around the visualization algorithm described here, is freely available (including commercial use) for Linux, MacOS, Windows and Android (Intel) from www.YASARA.org . Contact: elmar@yasara.org Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Cited by
Hoffmann, M., Kleine-Weber, H., & Pöhlmann, S. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.04.022 · Cited by 1,852
Grifoni, A., Sidney, J., Zhang, Y., Scheuermann, R. H., Peters, B., & Sette, A. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.03.002 · Cited by 940
A series of PDB-related databanks for everyday needs
Touw, W. G., Baakman, C., Black, J., te Beek, T. A. H., Krieger, E., Joosten, R. P., & Vriend, G. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1028 · Cited by 935
Self-citationAlphaFill: enriching AlphaFold models with ligands and cofactors
Hekkelman, M. L., de Vries, I., Joosten, R. P., & Perrakis, A. (2023) · Nature Methods · doi:10.1038/s41592-022-01685-y · Cited by 511
Gentile, D., Patamia, V., Scala, A., Sciortino, M. T., Piperno, A., & Rescifina, A. (2020) · Marine Drugs · doi:10.3390/md18040225 · Cited by 319
Metadata
- Authors
- Krieger, E., & Vriend, G.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-07-04
- Volume
- 30
- Issue
- 20
- Pages
- 2981-2982
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2154792548
- Cited by
- 1,568
- References
- 1
- FWCI
- 142.00
- Type
- journal article
- Language
- en
- Open access
- hybrid
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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