Dali/FSSP classification of three-dimensional protein folds
Open accessAbstract
The FSSP database presents a continuously updated structural classification of three-dimensional protein folds. It is derived using an automatic structure comparison program (Dali) for the all-against-all comparison of over 6000 three-dimensional coordinate sets in the Protein Data Bank (PDB). Sequence-related protein families are covered by a representative set of 813 protein chains. Hierachical clustering based on structural similarities yields a fold tree that defines 253 fold classes. For each representative protein chain, there is a database entry containing structure-structure alignments with its structural neighbours in the PDB. The database is accessible online through World Wide Web browsers and by anonymous ftp (file transfer protocol). The overview of fold space and the individual data sets provide a rich source of information for the study of both divergent and convergent aspects of molecular evolution, and define useful test sets and a standard of truth for assessing the correctness of sequence-sequence or sequence-structure alignments.
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Some of the armadillo repeats in the 'stem' subdomain display the structural features of HEAT repeats, as revealed by protein folding similarity searches using the Dali server.
“Some of the armadillo repeats in the 'stem' subdomain display the structural features of HEAT repeats, as revealed by protein folding similarity searches using the Dali server [33]”
From Oncoprotein CIP2A is stabilized via interaction with tumor suppressor PP2A/B56 (2017) · cites this paper as [33]
Cites
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Kraulis, P. J. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891004399 · Cited by 14,157 · see citing works
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,582 · see citing works
Murzin, A. G., Brenner, S. E., Hubbard, T., & Chothia, C. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80134-2 · Cited by 6,412 · see citing works
Protein Structure Comparison by Alignment of Distance Matrices
Holm, L., & Sander, C. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1489 · Cited by 3,984 · see citing works
Self-citationRASMOL: biomolecular graphics for all
Sayle, R. A. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89080-5 · Cited by 2,587 · see citing works
Introduction to Protein Structure
Brändén, C.-I., & Tooze, J. (2012) · Garland Science eBooks · doi:10.1201/9781136969898 · Cited by 2,398 · see citing works
Database of homology‐derived protein structures and the structural meaning of sequence alignment
Sander, C., & Schneider, R. (1991) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340090107 · Cited by 1,638 · see citing works
Self-citationHolm, L., & Sander, C. (1996) · Science · doi:10.1126/science.273.5275.595 · Cited by 1,504 · see citing works
Self-citationSurprising similarities in structure comparison
Gibrat, J.-F., Madej, T., & Bryant, S. H. (1996) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(96)80058-3 · Cited by 1,041 · see citing works
Prosite: a dictionary of sites and patterns in proteins
Bairoch, A. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.suppl.2013 · Cited by 930 · see citing works
Selection of representative protein data sets
Hobohm, U., Scharf, M. E., Schneider, R., & Sander, C. (1992) · Protein Science · doi:10.1002/pro.5560010313 · Cited by 818 · see citing works
Self-citationThe SWISS-PROT protein sequence data bank
Bairoch, A., & Boeckmann, B. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.suppl.2019 · Cited by 533 · see citing works
The FSSP database: fold classification based on structure-structure alignment of proteins
Holm, L. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.1.206 · Cited by 255 · see citing works
Self-citationIdentification and classification of protein fold families
Orengo, C. A., Flores, T. P., Taylor, W. R., et al. (1993) · Protein Engineering Design and Selection · doi:10.1093/protein/6.5.485 · Cited by 223 · see citing works
Crystal structure of the macrophage migration inhibitory factor from rat liver
Suzuki, M., Sugimoto, H., Nakagawa, A., Tanaka, I., Nishihira, J., & Sakai, M. (1996) · Nature Structural Biology · doi:10.1038/nsb0396-259 · Cited by 190 · see citing works
Identification and analysis of domains in proteins
Islam, S. A., Luo, J., & Sternberg, M. J. E. (1995) · Protein Engineering Design and Selection · doi:10.1093/protein/8.6.513 · Cited by 128 · see citing works
GeneQuiz: a workbench for sequence analysis.
Scharf, M. E., Schneider, R., Casari, G., Peer Bork, B., Valencia, A., Ouzounis, C. A., & Sander, C. (1994) · PubMed · Cited by 90 · see citing works
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Twilight zone of protein sequence alignments
Rost, B. (1999) · Protein Engineering, Design and Selection · doi:10.1093/protein/12.2.85 · Cited by 1,833 · see citing works
Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., & Koonin, E. V. (2006) · Biology Direct · doi:10.1186/1745-6150-1-7 · Cited by 1,199 · see citing works
Nuclear receptors CAR and PXR: Molecular, functional, and biomedical aspects
di Masi, A., Marinis, E. D., Ascenzi, P., & Marino, M. (2009) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2009.04.002 · Cited by 288 · see citing works
Oncoprotein CIP2A is stabilized via interaction with tumor suppressor PP2A/B56
Wang, J., Okkeri, J., Pavic, K., Wang, Z., Kauko, O., Halonen, T., Sarek, G., Ojala, P. M., Rao, Z., Xu, W., et al. (2017) · The EMBO Reports · doi:10.15252/embr.201642788 · Cited by 95 · see citing works
- Authors
- Holm, L., & Sander, C.
- Affiliations
- European Bioinformatics Institute (GB)
- Corresponding author
- Holm, L.
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1997-01-01
- Volume
- 25
- Issue
- 1
- Pages
- 231-234
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC146389
- OpenAlex
- W2137345862
- Cited by
- 421
- References
- 17
- Citations by year
- 2025: 4 · 2024: 4 · 2023: 4 · 2021: 1 · 2020: 6 · 2019: 5 · 2018: 3 · 2017: 3 · 2016: 9 · 2015: 5 · 2014: 4 · 2013: 6 · 2012: 4
- FWCI
- 8.18
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- protein fold classification, Dali, protein 3D structure, structural comparison, hierarchical clustering, Protein Data Bank, protein evolution
- MeSH terms
- Amino Acid Sequence, Animals, Molecular Sequence Data, Proteins, Databases, Factual, Sequence Alignment, Protein Folding
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