The Database of Interacting Proteins: 2004 update
Open accessAbstract
The Database of Interacting Proteins (http://dip.doe-mbi.ucla.edu) aims to integrate the diverse body of experimental evidence on protein-protein interactions into a single, easily accessible online database. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks.
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
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
SPRING-score and Z-score cutoffs were trained to optimize MCC for classifying interacting versus noninteracting protein pairs on a dataset of 1732 structurally characterized PPI pairs and 4117 noninteracting pairs.
“The Z-score and SPRING-score cutoffs were trained to optimize the Matthews correlation coefficient (MCC) of classifying interacting versus noninteracting protein pairs on a dataset consisting of 1732 structurally characterized PPI pairs from the SPRING dimer template database and 4117 pairs of noninteracting proteins from the Database of Interacting Proteins (DIP).51”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Functional organization of the yeast proteome by systematic analysis of protein complexes
Gavin, A., Böesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A., Cruciat, C., et al. (2002) · Nature · doi:10.1038/415141a · Cited by 4,729 · see citing works
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706 · see citing works
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Ho, Y., Gruhler, A., Heilbut, A. M., Bader, G. D., Moore, L., Adams, S., Millar, A., Taylor, P. P., Bennett, K. L., Boutilier, K., et al. (2002) · Nature · doi:10.1038/415180a · Cited by 3,573 · see citing works
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566 · see citing works
Comparative assessment of large-scale data sets of protein–protein interactions
von Mering, C., Krause, R., Snel, ., Cornell, M. J., Oliver, S. G., Fields, S., & Peer Bork, B. (2002) · Nature · doi:10.1038/nature750 · Cited by 2,339 · see citing works
Global Analysis of Protein Activities Using Proteome Chips
Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., et al. (2001) · Science · doi:10.1126/science.1062191 · Cited by 1,884 · see citing works
Xénarios, I. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.303 · Cited by 1,746 · see citing works
BIND--The Biomolecular Interaction Network Database
Bader, G. D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.242 · Cited by 1,556 · see citing works
DIP: the Database of Interacting Proteins
Xénarios, I. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.289 · Cited by 1,125 · see citing works
BIND: the Biomolecular Interaction Network Database
Bader, G. D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg056 · Cited by 1,113 · see citing works
Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S., & Sakaki, Y. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.3.1143 · Cited by 814 · see citing works
MINT: a Molecular INTeraction database
Zanzoni, A., Montecchi‐Palazzi, L., Quondam, M., Ausiello, G., Helmer‐Citterich, M., & Cesareni, G. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)03293-8 · Cited by 784 · see citing works
Protein function in the post-genomic era
Eisenberg, D. S., Marcotte, E. M., Xénarios, I., & Yeates, T. O. (2000) · Nature · doi:10.1038/35015694 · Cited by 749 · see citing works
Deane, C. M., Salwiński, Ł., Xénarios, I., & Eisenberg, D. S. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m100037-mcp200 · Cited by 645 · see citing works
Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt926 · Cited by 630 · see citing works
Self-citationInferring Domain–Domain Interactions From Protein–Protein InteractionsPreprint
Deng, M., Mehta, S., Sun, F., & Chen, T. (2002) · Genome Research · doi:10.1145/565196.565211 · Cited by 475 · see citing works
The Protein Data Bank: unifying the archive
Westbrook, J. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.245 · Cited by 309 · see citing works
Mining literature for protein–protein interactions
Marcotte, E. M., Xénarios, I., & Eisenberg, D. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.4.359 · Cited by 295 · see citing works
Costanzo, M. C. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.73 · Cited by 288 · see citing works
Is There a Bias in Proteome Research?Preprint
Mrowka, R., Patzak, A. R., & Herzel, H. (2001) · Genome Research · doi:10.1101/gr.206701 · Cited by 227 · see citing works
Computational methods of analysis of protein–protein interactions
Salwiński, Ł., & Eisenberg, D. S. (2003) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(03)00070-8 · Cited by 137 · see citing works
Analysis of gene expression data with pathway scores.
Zien, A., Küffner, R., Zimmer, R., & Lengauer, T. (2000) · PubMed · Cited by 120 · see citing works
Describing Biological Protein Interactions in Terms of Protein States and State Transitions
Duan, X. J., Xénarios, I., & Eisenberg, D. S. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m100026-mcp200 · Cited by 47 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., Bork, P., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1131 · Cited by 17,749 · see citing works
STRING v10: protein–protein interaction networks, integrated over the tree of life
Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1003 · Cited by 10,436 · see citing works
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1094 · Cited by 4,398 · see citing works
BioGRID: a general repository for interaction datasets
Stark, C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj109 · Cited by 3,960 · see citing works
Interaction network containing conserved and essential protein complexes in Escherichia coli
Butland, G., Peregrín-Alvarez, J. M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., et al. (2005) · Nature · doi:10.1038/nature03239 · Cited by 1,201 · see citing works
Flexible nets: The roles of intrinsic disorder in protein interaction networks
Dunker, A. K., Cortese, M. S., Romero, P., Iakoucheva, L. M., & Uversky, V. N. (2005) · The FEBS Journal · doi:10.1111/j.1742-4658.2005.04948.x · Cited by 1,122 · see citing works
Combinatorial drug therapy for cancer in the post-genomic era
Al-Lazikani, B., Banerji, U., & Workman, P. (2012) · Nature Biotechnology · doi:10.1038/nbt.2284 · Cited by 1,070 · see citing works
The BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745 · see citing works
ConsensusPathDB: toward a more complete picture of cell biology
Kamburov, A., Pentchev, K., Galicka, H., Wierling, C., Lehrach, H., & Herwig, R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1156 · Cited by 671 · see citing works
Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?
Keskin, O., Gursoy, A., Ma, B., & Nussinov, R. (2008) · Chemical Reviews · doi:10.1021/cr040409x · Cited by 697 · see citing works
The IntAct molecular interaction database in 2010
Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A. T., Kerrien, S., Khadake, J., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp878 · Cited by 620 · see citing works
Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt926 · Cited by 630 · see citing works
Self-citationConsensusPathDB--a database for integrating human functional interaction networks
Kamburov, A., Wierling, C., Lehrach, H., & Herwig, R. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn698 · Cited by 565 · see citing works
TRRUST: a reference database of human transcriptional regulatory interactions
Han, H., Shim, H., Shin, D., Shim, J. E., Ko, Y., Shin, J., Kim, H., Cho, A., Kim, E., Lee, T., et al. (2015) · Scientific Reports · doi:10.1038/srep11432 · Cited by 462 · see citing works
Interactome3D: adding structural details to protein networks
Mosca, R., Céol, A., & Aloy, P. (2013) · Nature Methods · doi:10.1038/nmeth.2289 · Cited by 479 · see citing works
The IntAct database: efficient access to fine-grained molecular interaction data
del Toro, N., Shrivastava, A., Ragueneau, E., Meldal, B., Combe, C., Barrera, E., Perfetto, L., How, K., Ratan, P., Shirodkar, G., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1006 · Cited by 405 · see citing works
Self-citationComplex cellular responses to reactive oxygen species
Temple, M. D., Perrone, G. G., & Dawes, I. W. (2005) · Trends in Cell Biology · doi:10.1016/j.tcb.2005.04.003 · Cited by 398 · see citing works
Predicting Protein–Protein Interactions from the Molecular to the Proteome Level
Keskin, O., Tuncbag, N., & Gursoy, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00683 · Cited by 369 · see citing works
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes
Huang, J. K., Carlin, D. E., Yu, M. K., Zhang, W., Kreisberg, J. F., Tamayo, P., & Ideker, T. (2018) · Cell Systems · doi:10.1016/j.cels.2018.03.001 · Cited by 289 · see citing works
Bhasin, M. K., Dusek, J. A., Chang, B.-H., Joseph, M. G., Denninger, J. W., Fricchione, G. L., Benson, H., & Libermann, T. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062817 · Cited by 304 · see citing works
Granneman, J. G., Li, P., Zhu, Z., & Lu, Y. (2005) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00009.2005 · Cited by 298 · see citing works
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
Kerrien, S., Orchard, S., Montecchi-Palazzi, L., Aranda, B., Quinn, A. F., Vinod, N., Bader, G. D., Xenarios, I., Wojcik, J., Sherman, D., et al. (2007) · BMC Biology · doi:10.1186/1741-7007-5-44 · Cited by 266 · see citing works
Self-citationA Systems Biology Approach for the Investigation of the Heparin/Heparan Sulfate Interactome
Ori, A., Wilkinson, M. C., & Fernig, D. G. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.228114 · Cited by 251 · see citing works
Wei, L., Xing, P., Zeng, J., Chen, J., Su, R., & Guo, F. (2017) · Artificial Intelligence in Medicine · doi:10.1016/j.artmed.2017.03.001 · Cited by 242 · see citing works
Human Cancer Protein-Protein Interaction Network: A Structural Perspective
Kar, G., Gursoy, A., & Keskin, O. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000601 · Cited by 235 · see citing works
Tau Protein Interaction Partners and Their Roles in Alzheimer’s Disease and Other Tauopathies
Sinsky, J., Pichlerova, K., & Hanes, J. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22179207 · Cited by 220 · see citing works
Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps
Huang, H., Jedynak, B. M., & Bader, J. S. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030214 · Cited by 182 · see citing works
Templates are available to model nearly all complexes of structurally characterized proteins
Kundrotas, P. J., Zhu, Z., Janin, J., & Vakser, I. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1200678109 · Cited by 179 · see citing works
Identification of disease treatment mechanisms through the multiscale interactome
Ruiz, C., Zitnik, M., & Leskovec, J. (2021) · Nature Communications · doi:10.1038/s41467-021-21770-8 · Cited by 172 · see citing works
Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Nisanci, G., Cetin-Atalay, R., & Ozturk, M. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.7.996 · Cited by 156 · see citing works
Pathway information for systems biology
Cary, M. P., Bader, G. D., & Sander, C. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.02.005 · Cited by 152 · see citing works
MedlineRanker: flexible ranking of biomedical literature
Fontaine, J.-F., Barbosa-Silva, A., Schaefer, M., Huska, M. R., Muro, E. M., & Andrade-Navarro, M. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp353 · Cited by 147 · see citing works
Exploration of databases and methods supporting drug repurposing: a comprehensive survey
Tanoli, Z., Seemab, U., Scherer, A., Wennerberg, K., Tang, J., & Vähä-Koskela, M. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa003 · Cited by 131 · see citing works
cPath: open source software for collecting, storing, and querying biological pathways
Cerami, E. G., Bader, G. D., Gross, B. E., & Sander, C. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-497 · Cited by 125 · see citing works
Lum, K. K., & Cristea, I. M. (2016) · Expert Review of Proteomics · doi:10.1586/14789450.2016.1147353 · Cited by 113 · see citing works
Miteva, Y. V., Budayeva, H. G., & Cristea, I. M. (2013) · Analytical Chemistry · doi:10.1021/ac3033257 · Cited by 105 · see citing works
LRRK2 mediates microglial neurotoxicity via NFATc2 in rodent models of synucleinopathies
Kim, C., Beilina, A., Smith, N., Li, Y., Kim, M., Kumaran, R., Kaganovich, A., Mamais, A., Adame, A., Iba, M., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aay0399 · Cited by 79 · see citing works
Albaradei, S., Napolitano, F., Thafar, M. A., Gojobori, T., Essack, M., & Gao, X. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.08.006 · Cited by 61 · see citing works
PINA 3.0: mining cancer interactome
Du, Y., Cai, M., Xing, X., Ji, J., Yang, E., & Wu, J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1075 · Cited by 60 · see citing works
Afroz, S., Giddaluru, J., Vishwakarma, S., Naz, S., Khan, A. A., & Khan, N. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00074 · Cited by 50 · see citing works
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases
Zolotareva, O., & Kleine, M. (2019) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2018-0069 · Cited by 46 · see citing works
Li, S., Wu, S., Wang, L., Li, F., Jiang, H., & Bai, F. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102344 · Cited by 42 · see citing works
RAPPPID: towards generalizable protein interaction prediction with AWD-LSTM twin networks
Szymborski, J., & Emad, A. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac429 · Cited by 34 · see citing works
Zhang, C., Zheng, W., Cheng, M., Omenn, G. S., Freddolino, P. L., & Zhang, Y. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00359 · Cited by 27 · see citing works
Network-Free Inference of Knockout Effects in Yeast
Peleg, T., Yosef, N., Ruppin, E., & Sharan, R. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000635 · Cited by 14 · see citing works
Jung, S., Singh, K., & del Sol, A. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa283 · Cited by 9 · see citing works
Structure-Based Deep Learning Framework for Modeling Human–Gut Bacterial Protein Interactions
Kiouri, D. P., Batsis, G. C., & Chasapis, C. T. (2025) · Proteomes · doi:10.3390/proteomes13010010 · Cited by 3 · see citing works
- Authors
- Salwinski, L.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-01-01
- Volume
- 32
- Issue
- 90001
- Pages
- 449D-451
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC308820
- OpenAlex
- W2130687290
- Cited by
- 2,271
- References
- 23
- Citations by year
- 2026: 20 · 2025: 27 · 2024: 44 · 2023: 50 · 2022: 72 · 2021: 84 · 2020: 116 · 2019: 87 · 2018: 94 · 2017: 101 · 2016: 101 · 2015: 108 · 2014: 87 · 2013: 137 · 2012: 160
- FWCI
- 28.38
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Energy
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Keywords
- protein-protein interaction, core set, high-throughput interaction data, protein-protein interaction network, interaction prediction
- MeSH terms
- Animals, Humans, Protein Binding, Proteins, Reproducibility of Results, Information Storage and Retrieval, Computational Biology, Internet, Databases, Protein, Macromolecular Substances
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
