The DOI matches its Crossref record; 26 of the 26 references it cites were found in a registry or an index.
ProFunc: a server for predicting protein function from 3D structure
Open accessAbstract
ProFunc (http://www.ebi.ac.uk/thornton-srv/databases/ProFunc) is a web server for predicting the likely function of proteins whose 3D structure is known but whose function is not. Users submit the coordinates of their structure to the server in PDB format. ProFunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. A summary of the analyses provides an at-a-glance view of what each of the different methods has found. More detailed results are available on separate pages. Often where one method has failed to find anything useful another may be more forthcoming. The server is likely to be of most use in structural genomics where a large proportion of the proteins whose structures are solved are of hypothetical proteins of unknown function. However, it may also find use in a comparative analysis of members of large protein families. It provides a convenient compendium of sequence and structural information that often hold vital functional clues to be followed up experimentally.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
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
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
UniProt: the Universal Protein knowledgebase
Apweiler, R. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh131 · Cited by 7,498
InterProScan – an integration platform for the signature-recognition methods in InterPro
Zdobnov, E. M., & Apweiler, R. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.9.847 · Cited by 2,939
RASMOL: biomolecular graphics for all
Sayle, R. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89080-5 · Cited by 2,575
PISCES: a protein sequence culling server
Wang, G., & Dunbrack, R. L. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg224 · Cited by 1,662
Glaser, F., Pupko, T., Paz, I., Bell, R. E., Bechor-Shental, D., Martz, E., & Ben-Tal, N. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.1.163 · Cited by 1,236
An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families
Lichtarge, O., Bourne, H. R., & Cohen, F. E. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0167 · Cited by 1,195
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
Laskowski, R. A. (1995) · Journal of Molecular Graphics · doi:10.1016/0263-7855(95)00073-9 · Cited by 1,002
Self-citation
Cited by
Dali server: conservation mapping in 3D
Holm, L., & Rosenstr�m, P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq366 · Cited by 3,640
Automated protein function prediction--the genomic challenge
Friedberg, I. (2006) · Briefings in Bioinformatics · doi:10.1093/bib/bbl004 · Cited by 366
Protein Function Prediction Using Local 3D Templates
Laskowski, R. A., Watson, J. D., & Thornton, J. M. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.05.067 · Cited by 213
Self-citationA topological approach for protein classification
Cang, Z., Mu, L., Wu, K., Opron, K., Xia, K., & Wei, G.-W. (2015) · Computational and Mathematical Biophysics · doi:10.1515/mlbmb-2015-0009 · Cited by 93
Boadu, F., Cao, H., & Cheng, J. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad208 · Cited by 81
Metadata
- Authors
- Laskowski, R. A., Watson, J. D., & Thornton, J. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-07-01
- Volume
- 33
- Issue
- Web Server
- Pages
- W89-W93
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2100494857
- Cited by
- 655
- References
- 26
- FWCI
- 13.48
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: ProFunc: a server for predicting protein function from 3D structure. https://app.cochat.ai/papers/10.1093/nar/gki414
- The paper
- Laskowski, R. A., Watson, J. D., & Thornton, J. M. (2005). ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Research. https://doi.org/10.1093/nar/gki414
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
