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Wordom: a program for efficient analysis of molecular dynamics simulations
Open accessAbstract
Summary: Wordom is a versatile program for manipulation of molecular dynamics trajectories and efficient analysis of simulations. Original tools in Wordom include a procedure to evaluate significance of sampling for principal component analysis as well as modules for clustering multiple conformations and evaluation of order parameters for folding and aggregation. The program was developed with special emphasis on user-friendliness, effortless addition of new modules and efficient handling of large sets of trajectories. Availability: The Wordom program is distributed with full source code (in the C language) and documentation for usage and further development as a platform-independent package under a GPL license from http://www.biochem-caflisch.unizh.ch/wordom/ Contact: caflisch@bioc.unizh.ch
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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
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A gating mechanism of pentameric ligand-gated ion channels
Calimet, N., Simoes, M., Changeux, J.-P., Karplus, M., Taly, A., & Cecchini, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313785110 · Cited by 150
Self-citationThe Free Energy Landscape of Small Molecule Unbinding
Huang, D., & Caflisch, A. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002002 · Cited by 116
Self-citationMartin, N. E., Malik, S., Calimet, N., Changeux, J.-P., & Cecchini, M. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005784 · Cited by 38
Self-citationMolecular Mechanisms of the R61T Mutation in Apolipoprotein E4: A Dynamic Rescue
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Metadata
- Authors
- Seeber, M., Cecchini, M., Rao, F., Settanni, G., & Caflisch, A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-08-23
- Volume
- 23
- Issue
- 19
- Pages
- 2625-2627
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2139561304
- Cited by
- 275
- References
- 1
- FWCI
- 5.39
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Seeber, M., Cecchini, M., Rao, F., Settanni, G., & Caflisch, A. (2007). Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinformatics. https://doi.org/10.1093/bioinformatics/btm378
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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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