The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
The RCSB Protein Data Bank: redesigned web site and web services
Open accessAbstract
The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education.
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Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Announcing the worldwide Protein Data Bank
Berman, H., Henrick, K., & Nakamura, H. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb1203-980 · Cited by 3,093
Self-citationThe Pfam protein families database
Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp985 · Cited by 2,694
Crystal structure of the ribosome at 5.5 Å resolution
Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. D., & Noller, H. F. (2001) · Science · doi:10.1126/science.1060089 · Cited by 1,944
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HMMER web server: interactive sequence similarity searching
Finn, R. D., Clements, J., & Eddy, S. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr367 · Cited by 5,952
Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Christie, C. H., Dalenberg, K., Di Costanzo, L., Duarte, J. M., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1038 · Cited by 1,581
Self-citationD2P2: database of disordered protein predictions
Oates, M. E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M. J., Xue, B., Dosztányi, Z., Uversky, V. N., Obradovic, Z., Kurgan, L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1226 · Cited by 705
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APPRIS: annotation of principal and alternative splice isoforms
Rodriguez, J. M., Maietta, P., Ezkurdia, I., Pietrelli, A., Wesselink, J.-J., Lopez, G., Valencia, A., & Tress, M. L. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks1058 · Cited by 232
In silico method for modelling metabolism and gene product expression at genome scale
Lerman, J. A., Hyduke, D. R., Latif, H., Portnoy, V. A., Lewis, N. E., Orth, J. D., Schrimpe-Rutledge, A. C., Smith, R. D., Adkins, J. N., Zengler, K., et al. (2012) · Nature Communications · doi:10.1038/ncomms1928 · Cited by 266
The role of protonation states in ligand-receptor recognition and binding.
Petukh, M., Stefl, S., & Alexov, E. (2013) · Current Pharmaceutical Design · doi:10.2174/1381612811319230004 · Cited by 101
Skolnick, J., Zhou, H., & Brylinski, M. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp211052j · Cited by 35
ZnuD, a Potential Candidate for a Simple and Universal Neisseria meningitidis Vaccine
Hubert, K., Devos, N., Mordhorst, I., Tans, C., Baudoux, G., Feron, C., Goraj, K., Tommassen, J., Vogel, U., Poolman, J. T., et al. (2013) · Infection and Immunity · doi:10.1128/iai.01312-12 · Cited by 28
Metadata
- Authors
- Rose, P. W., Beran, B., Bi, C., Bluhm, W. F., Dimitropoulos, D., Goodsell, D. S., Prlic, A., Quesada, M., Quinn, G. B., Westbrook, J. D., Young, J., Yukich, B., Zardecki, C., Berman, H. M., & Bourne, P. E.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-10-29
- Volume
- 39
- Issue
- Database
- Pages
- D392-D401
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2170441710
- Cited by
- 658
- References
- 4
- FWCI
- 36.60
- Type
- journal article
- Language
- en
- Open access
- gold
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