The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
3V: cavity, channel and cleft volume calculator and extractor
Open accessAbstract
As larger macromolecular structures become available, there is a growing need to understand their 'internal' volumes--such as deep clefts, channels and cavities--as these often play critical roles in their function. The 3V web server can automatically extract and comprehensively analyze all the internal volumes from input RNA and protein structures. It rapidly finds internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces, one with as large as possible a probe radius and the other with a solvent radius (typically 1.5 A for water). The outputs are volumetric representations, both as images and downloadable files, which can be used for further analysis. The 3V server and source code are available from http://3vee.molmovdb.org.
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Cites
Structure of P-Glycoprotein Reveals a Molecular Basis for Poly-Specific Drug Binding
Aller, S. G., Yu, J., Ward, A., Weng, Y., Chittaboina, S., Zhuo, R., Harrell, P. M., Trinh, Y. T., Zhang, Q., Urbatsch, I. L., et al. (2009) · Science · doi:10.1126/science.1168750 · Cited by 1,929
Cited by
Cassago, A., Ferreira, A. P. S., Ferreira, I. M., Fornezari, C., Gomes, E. R. M., Greene, K. S., Pereira, H. M., Garratt, R. C., Dias, S. M. G., & Ambrosio, A. L. B. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1112495109 · Cited by 285
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport
Stourac, J., Vavra, O., Kokkonen, P., Filipovic, J., Pinto, G., Brezovsky, J., Damborsky, J., & Bednar, D. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz378 · Cited by 267
Structure of the STRA6 receptor for retinol uptake
Chen, Y., Clarke, O. B., Kim, J., Stowe, S., Kim, Y.-K., Assur, Z., Cavalier, M., Godoy-Ruiz, R., von Alpen, D. C., Manzini, C., et al. (2016) · Science · doi:10.1126/science.aad8266 · Cited by 148
Prediction of site-specific interactions in antibody–antigen complexes: the proABC method and server
Olimpieri, P. P., Chailyan, A., Tramontano, A., & Marcatili, P. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt369 · Cited by 90
Determining crystal structures through crowdsourcing and coursework
Horowitz, S., Koepnick, B., Martin, R., Tymieniecki, A., Winburn, A. A., Cooper, S., Flatten, J., Rogawski, D. S., Koropatkin, N. M., Hailu, T. T., et al. (2016) · Nature Communications · doi:10.1038/ncomms12549 · Cited by 75
Metadata
- Authors
- Voss, N. R., & Gerstein, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-05-16
- Volume
- 38
- Issue
- Web Server
- Pages
- W555-W562
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2169242540
- Cited by
- 476
- References
- 1
- FWCI
- 6.50
- Type
- journal article
- Language
- en
- Open access
- gold
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