Computed cancer interactome explains the effects of somatic mutations in cancers
Open accessPublished version of a preprint
Abstract
Protein–protein interactions (PPIs) are involved in almost all essential cellular processes. Perturbation of PPI networks plays critical roles in tumorigenesis, cancer progression, and metastasis. While numerous high‐throughput experiments have produced a vast amount of data for PPIs, these data sets suffer from high false positive rates and exhibit a high degree of discrepancy. Coevolution of amino acid positions between protein pairs has proven to be useful in identifying interacting proteins and providing structural details of the interaction interfaces with the help of deep learning methods like AlphaFold (AF). In this study, we applied AF to investigate the cancer protein–protein interactome. We predicted 1,798 PPIs for cancer driver proteins involved in diverse cellular processes such as transcription regulation, signal transduction, DNA repair, and cell cycle. We modeled the spatial structures for the predicted binary protein complexes, 1,087 of which lacked previous 3D structure information. Our predictions offer novel structural insight into many cancer‐related processes such as the MAP kinase cascade and Fanconi anemia pathway. We further investigated the cancer mutation landscape by mapping somatic missense mutations (SMMs) in cancer to the predicted PPI interfaces and performing enrichment and depletion analyses. Interfaces enriched or depleted with SMMs exhibit different preferences for functional categories. Interfaces enriched in mutations tend to function in pathways that are deregulated in cancers and they may help explain the molecular mechanisms of cancers in patients; interfaces lacking mutations appear to be essential for the survival of cancer cells and thus may be future targets for PPI modulating drugs.
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Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works
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 · see citing works
Hallmarks of Cancer: The Next Generation
Hanahan, D., & Weinberg, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.02.013 · Cited by 66,590 · see citing works
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890 · see citing works
Cd-hit: Accelerated for clustering the next-generation sequencing data
Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175 · see citing works
Mutations of the BRAF gene in human cancer
Davies, H., Bignell, G. R., Cox, C., Stephens, P., Edkins, S., Clegg, S., Teague, J., Woffendin, H., Garnett, M. J., Bottomley, W., et al. (2002) · Nature · doi:10.1038/nature00766 · Cited by 10,674 · see citing works
The mutational constraint spectrum quantified from variation in 141,456 humans
Karczewski, K. J., Francioli, L. C., Tiao, G., Cummings, B. B., Alföldi, J., Wang, Q., Collins, R. L., Laricchia, K. M., Ganna, A., Birnbaum, D. P., et al. (2020) · Nature · doi:10.1038/s41586-020-2308-7 · Cited by 9,434 · see citing works
The cancer genome atlas pan-cancer analysis project
The Cancer Genome Atlas Research Network, Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Shmulevich, I., Sander, C., & Stuart, J. M. (2013) · Nature Genetics · doi:10.1038/ng.2764 · Cited by 9,092 · see citing works
Vogelstein, B., Papadopoulos, N., Velculescu, V. E., Zhou, S., Diaz, L. A., & Kinzler, K. W. (2013) · Science · doi:10.1126/science.1235122 · Cited by 7,863 · see citing works
Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850 · see citing works
UniProt: the universal protein knowledgebase in 2021
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1100 · Cited by 6,372 · see citing works
Accurate prediction of protein structures and interactions using a 3-track network
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,542 · see citing works
Self-citationThe Somatic Genomic Landscape of Glioblastoma
Brennan, C. W., Verhaak, R. G. W., McKenna, A., Campos, B., Noushmehr, H., Salama, S. R., Zheng, S., Chakravarty, D., Sanborn, J. Z., Berman, S. H., et al. (2013) · Cell · doi:10.1016/j.cell.2013.09.034 · Cited by 5,016 · see citing works
COSMIC: the Catalogue Of Somatic Mutations In Cancer
Tate, J. G., Bamford, S., Jubb, H. C., Sondka, Z., Beare, D. M., Bindal, N., Boutselakis, H., Cole, C. G., Creatore, C., Dawson, E., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1015 · Cited by 4,867 · see citing works
Highly accurate protein structure prediction for the human proteome
Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025 · cited 1× · see citing works
“significantly expanded the capability of obtaining high-resolution protein structures [31] and interactions [32].”
BackgroundTowards a proteome-scale map of the human protein–protein interaction network
Rual, J.-F. M., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., et al. (2005) · Nature · doi:10.1038/nature04209 · Cited by 2,904 · see citing works
International network of cancer genome projects
The International Cancer Genome Consortium (2010) · Nature · doi:10.1038/nature08987 · Cited by 2,299 · see citing works
Self-citationComprehensive Characterization of Cancer Driver Genes and Mutations
Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.060 · Cited by 2,256 · see citing works
Self-citationA Comprehensive Survey of Ras Mutations in Cancer
Prior, I. A., Lewis, P. D., & Mattos, C. (2012) · Cancer Research · doi:10.1158/0008-5472.can-11-2612 · Cited by 2,063 · see citing works
Reaching for high-hanging fruit in drug discovery at protein–protein interfaces
Wells, J. A., & McClendon, C. L. (2007) · Nature · doi:10.1038/nature06526 · Cited by 1,963 · see citing works
Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer
Ciriello, G., Gatza, M. L., Beck, A. H., Wilkerson, M. D., Rhie, S. K., Pastore, A., Zhang, H., McLellan, M. D., Yau, C. S. F., Kandoth, C., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.033 · Cited by 1,836 · see citing works
Cancer Susceptibility and the Functions of BRCA1 and BRCA2
Venkitaraman, A. R. (2002) · Cell · doi:10.1016/s0092-8674(02)00615-3 · Cited by 1,713 · see citing works
Pereira, B., Chin, S., Rueda, O. M., Vollan, H. K. M., Provenzano, E., Bardwell, H. A., Pugh, M., Jones, L. R., Russell, R., Sammut, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms11479 · Cited by 1,712 · see citing works
DNA repair pathways as targets for cancer therapy
Helleday, T., Petermann, E., Lundin, C., Hodgson, B., & Sharma, R. A. (2008) · Nature Reviews Cancer · doi:10.1038/nrc2342 · Cited by 1,666 · see citing works
The ATM protein kinase: regulating the cellular response to genotoxic stress, and more
Shiloh, Y., & Ziv, Y. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3546 · Cited by 1,649 · see citing works
The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers
Sondka, Z., Bamford, S., Cole, C. G., Ward, S. A., Dunham, I., & Forbes, S. A. (2018) · Nature Reviews Cancer · doi:10.1038/s41568-018-0060-1 · Cited by 1,597 · see citing works
The BioGRID interaction database: 2019 update
Oughtred, R., Stark, C., Breitkreutz, B., Rust, J., Boucher, L., Chang, C., Kolas, N. K., O’Donnell, L., Leung, G. C., McAdam, R. F., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1079 · Cited by 1,440 · see citing works
A Proteome-Scale Map of the Human Interactome Network
Rolland, T., Taşan, M., Charloteaux, B., Pevzner, S. J., Zhong, Q., Sahni, N., Yi, S. S., Lemmens, I. H., Fontanillo, C., Mosca, R., et al. (2014) · Cell · doi:10.1016/j.cell.2014.10.050 · Cited by 1,342 · see citing works
Perturbations of the AKT signaling pathway in human cancer
Altomare, D. A., & Testa, J. R. (2005) · Oncogene · doi:10.1038/sj.onc.1209085 · Cited by 1,326 · see citing works
CORUM: the comprehensive resource of mammalian protein complexes—2009
Ruepp, A., Wägele, B., Lechner, M., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C., & Mewes, H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp914 · Cited by 1,320 · see citing works
Calnan, D. R., & Brunet, A. (2008) · Oncogene · doi:10.1038/onc.2008.21 · Cited by 1,170 · see citing works
Kriventseva, E. V., Kuznetsov, D. A., Tegenfeldt, F., Manni, M., Dias, R. O., Simão, F. A., & Zdobnov, E. M. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1053 · Cited by 1,138 · 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
Bmi-1 collaborates with c-Myc in tumorigenesis by inhibiting c-Myc-induced apoptosis via INK4a/ARFPreprint
Jacobs, J. J. L., Scheijen, B., Voncken, J. W., Kieboom, K., Berns, A. J. M., & van Lohuizen, M. (1999) · Genes & Development · doi:10.1101/gad.13.20.2678 · Cited by 1,060 · see citing works
DNA repair dysregulation from cancer driver to therapeutic target
Curtin, N. J. (2012) · Nature Reviews Cancer · doi:10.1038/nrc3399 · Cited by 1,051 · see citing works
IntAct: an open source molecular interaction database
Hermjakob, H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh052 · Cited by 1,013 · see citing works
BRCA1 and BRCA2: 1994 and beyond
Narod, S. A., & Foulkes, W. D. (2004) · Nature Reviews Cancer · doi:10.1038/nrc1431 · Cited by 967 · see citing works
Lu, H., Zhou, Q., He, J., Jiang, Z., Peng, C., Tong, R., & Shi, J. (2020) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-020-00315-3 · Cited by 891 · see citing works
Control of BRCA2 Cellular and Clinical Functions by a Nuclear Partner, PALB2
Xia, B., Sheng, Q., Nakanishi, K., Ohashi, A., Wu, J., Christ, N., Liu, X., Jasin, M., Couch, F. J., & Livingston, D. M. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.05.022 · Cited by 861 · see citing works
Frank, T. S. (2002) · Journal of Clinical Oncology · doi:10.1200/jco.20.6.1480 · Cited by 813 · see citing works
Chang, M. T., Asthana, S., Gao, S. P., Lee, B. H., Chapman, J. S., Kandoth, C., Gao, J., Socci, N. D., Solit, D. B., Olshen, A. B., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3391 · Cited by 808 · 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
Cyclin D-dependent kinases, INK4 inhibitors and cancer
Ortega, S., Malumbres, M., & Barbacid, M. (2002) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/s0304-419x(02)00037-9 · Cited by 774 · see citing works
Identification of a RING protein that can interact in vivo with the BRCA1 gene product
Wu, L. C., Wang, Z. W., Tsan, J. T., Spillman, M. A., Phung, A., Xu, X. L., Yang, M.-C. W., Hwang, L.-Y., Bowcock, A. M., & Baer, R. J. (1996) · Nature Genetics · doi:10.1038/ng1296-430 · Cited by 743 · see citing works
The Fanconi anaemia pathway: new players and new functions
Ceccaldi, R., Sarangi, P., & D’Andrea, A. D. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.48 · Cited by 705 · see citing works
PALB2 is an integral component of the BRCA complex required for homologous recombination repair
Sy, S. M.-H., Huen, M. S. Y., & Chen, J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811159106 · Cited by 607 · see citing works
CORUM: the comprehensive resource of mammalian protein complexes—2019
Giurgiu, M., Reinhard, J., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C., & Ruepp, A. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky973 · Cited by 595 · see citing works
FOXOs, cancer and regulation of apoptosis
Fu, Z., & Tindall, D. J. (2008) · Oncogene · doi:10.1038/onc.2008.24 · Cited by 584 · see citing works
Monocyte heterogeneity and functions in cancer
Olingy, C. E., Dinh, H. Q., & Hedrick, C. C. (2019) · Journal of Leukocyte Biology · doi:10.1002/jlb.4ri0818-311r · Cited by 583 · see citing works
Frank, T. S., Deffenbaugh, A. M., Reid, J., Hulick, M., Ward, B. E., Lingenfelter, B., Gumpper, K. L., Scholl, T., Tavtigian, S. V., Pruss, D., et al. (2002) · Journal of Clinical Oncology · doi:10.1200/jco.2002.20.6.1480 · Cited by 557 · see citing works
PALB2 Links BRCA1 and BRCA2 in the DNA-Damage Response
Zhang, F., Ma, J., Wu, J., Ye, L., Cai, H., Xia, B., & Yu, X. (2009) · Current Biology · doi:10.1016/j.cub.2009.02.018 · Cited by 556 · see citing works
Computed structures of core eukaryotic protein complexes
Humphreys, I. R., Pei, J., Baek, M., Krishnakumar, A., Anishchenko, I., Ovchinnikov, S., Zhang, J., Ness, T. J., Banjade, S., Bagde, S. R., et al. (2021) · Science · doi:10.1126/science.abm4805 · Cited by 542 · see citing works
Self-citationRusso, A. A., Tong, L., Lee, J.-O., Jeffrey, P. D., & Pavletich, N. P. (1998) · Nature · doi:10.1038/26155 · Cited by 524 · see citing works
Structure of a BRCA1-BARD1 heterodimeric RING-RING complex.
Brzović, P. S., Rajagopal, P., Hoyt, D. W., King, M., & Klevit, R. E. (2001) · Nature Structural Biology · doi:10.1038/nsb1001-833 · Cited by 494 · see citing works
Global topological features of cancer proteins in the human interactome
Jonsson, P. F., & Bates, P. A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl390 · Cited by 490 · see citing works
The human Mi-2/NuRD complex and gene regulation
Denslow, S. A., & Wade, P. A. (2007) · Oncogene · doi:10.1038/sj.onc.1210611 · Cited by 479 · see citing works
The myc Oncogene: arvelouslomplex
Oster, S. K., Ho, C. S. W., Soucie, E. L., & Penn, L. Z. (2002) · Advances in cancer research · doi:10.1016/s0065-230x(02)84004-0 · Cited by 459 · see citing works
Docking domains and substrate-specificity determination for MAP kinases
Sharrocks, A. D., Yang, S.-H., & Galanis, A. (2000) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01627-3 · Cited by 442 · see citing works
Jacobs, D., Glossip, D., Xing, H., Muslin, A. J., & Kornfeld, K. (1999) · Genes & Development · doi:10.1101/gad.13.2.163 · Cited by 439 · see citing works
B lymphocytes and cancer: a love-hate relationship
Yuen, G. J., Demissie, E., & Pillai, S. (2016) · Trends in cancer · doi:10.1016/j.trecan.2016.10.010 · Cited by 433 · see citing works
Fekairi, S., Scaglione, S., Chahwan, C., Taylor, E. R., Tissier, A., Coulon, S., Dong, M., Ruse, C. I., Yates, J. R., Russell, P. R., et al. (2009) · Cell · doi:10.1016/j.cell.2009.06.029 · Cited by 418 · see citing works
Stanković, T., Kidd, A., Sutcliffe, A., McGuire, G. M., Robinson, P. N., Weber, P., Bedenham, T., Bradwell, A. R., Easton, D. F., Lennox, G. G., et al. (1998) · The American Journal of Human Genetics · doi:10.1086/301706 · Cited by 401 · see citing works
Targeting protein–protein interactions as an anticancer strategy
Ivanov, A. A., Khuri, F. R., & Fu, H. (2013) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2013.04.007 · Cited by 401 · see citing works
Mutations of the SLX4 gene in Fanconi anemia
Kim, Y., Lach, F. P., Desetty, R. D., Hanenberg, H., Auerbach, A. D., & Smogorzewska, A. (2011) · Nature Genetics · doi:10.1038/ng.750 · Cited by 372 · see citing works
BRCA2 mutations in primary breast and ovarian cancers
Lancaster, J. M., Wooster, R., Mangion, J., Phelan, C. M., Cochran, C., Gumbs, C. E., Seal, S., Barfoot, R., Collins, N., Bignell, G. R., et al. (1996) · Nature Genetics · doi:10.1038/ng0696-238 · Cited by 360 · see citing works
The Tumor Suppressor Protein p16INK4a
Serrano, M. (1997) · Experimental Cell Research · doi:10.1006/excr.1997.3824 · Cited by 346 · see citing works
AKT proto-oncogene overexpression is an early event during sporadic colon carcinogenesis
Roy, H. K. (2002) · Carcinogenesis · doi:10.1093/carcin/23.1.201 · Cited by 342 · see citing works
Making sense of cancer genomic dataPreprint
Chin, L., Hahn, W. C., Getz, G. A., & Meyerson, M. M. (2011) · Genes & Development · doi:10.1101/gad.2017311 · Cited by 336 · see citing works
Mutations in ERCC4, encoding the DNA-repair endonuclease XPF, cause Fanconi anemia.
Bogliolo, M., Schuster, B., Stoepker, C., Derkunt, B., Su, Y., Raams, A., Trujillo, J. P., Minguillón, J., Ramírez, M., Pujol, R., et al. (2013) · American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.04.002 · Cited by 334 · see citing works
MAX Mutations Cause Hereditary and Sporadic Pheochromocytoma and Paraganglioma
Burnichon, N., Cascón, A., Schiavi, F., Morales, N. P., Comino‐Méndez, I., Abermil, N., Inglada‐Pérez, L., de Cubas, A. A., Amar, L., Barontini, M., et al. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-0160 · Cited by 331 · see citing works
Targeting DNA damage response in cancer therapy
Hosoya, N., & Miyagawa, K. (2014) · Cancer Science · doi:10.1111/cas.12366 · Cited by 295 · see citing works
Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1.
Williams, R. S., Green, R., & Glover, J. N. M. (2001) · Nature Structural Biology · doi:10.1038/nsb1001-838 · Cited by 292 · see citing works
MAP kinase pathways: The first twenty years
Avruch, J. (2006) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2006.11.006 · Cited by 283 · see citing works
GLay: community structure analysis of biological networks
Su, G., Kuchinsky, A., Morris, J., States, D., & Meng, F. (2010) · Bioinform. · doi:10.1093/bioinformatics/btq596 · Cited by 273 · see citing works
Towards a structurally resolved human protein interaction network
Burke, D. F., Bryant, P., Barrio-Hernandez, I., Memon, D., Pozzati, G., Shenoy, A., Zhu, W., Dunham, A. S., Albanese, P., Keller, A., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00910-8 · Cited by 269 · see citing works
FANCM Connects the Genome Instability Disorders Bloom's Syndrome and Fanconi Anemia
Deans, A. J., & West, S. C. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.12.006 · Cited by 245 · see citing works
Clapperton, J. A., Manke, I. A., Lowery, D. M., Ho, T., Haire, L. F., Yaffe, M. B., & Smerdon, S. J. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb775 · Cited by 243 · see citing works
Structural basis of inhibition of CDK–cyclin complexes by INK4 inhibitorsPreprint
Jeffrey, P. D., Tong, L., & Pavletich, N. P. (2000) · Genes & Development · doi:10.1101/gad.851100 · Cited by 239 · see citing works
Weis, K. E., Ekena, K., Thomas, J. A., Lazennec, G., & Katzenellenbogen, B. S. (1996) · Molecular Endocrinology · doi:10.1210/mend.10.11.8923465 · Cited by 236 · see citing works
Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1
Williams, R. S., Lee, M. S., Hau, D. D., & Glover, J. N. M. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb776 · Cited by 230 · see citing works
Li, Z., Ivanov, A. A., Su, R., González-Pecchi, V., Qi, Q., Liu, S., Webber, P. J., McMillan, E. A., Rusnak, L. E., Pham, C., et al. (2017) · Nature Communications · doi:10.1038/ncomms14356 · Cited by 227 · see citing works
Comprehensive assessment of cancer missense mutation clustering in protein structures
Kamburov, A., Lawrence, M. S., Polak, P. P., Leshchiner, I., Lage, K., Golub, T. R., Lander, E. S., & Getz, G. A. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1516373112 · Cited by 218 · see citing works
3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets
Gao, J., Chang, M. T., Johnsen, H. C., Gao, S. P., Sylvester, B. E., Sümer, S. O., Zhang, H., Solit, D. B., Taylor, B. S., Schultz, N. D., et al. (2017) · Genome Medicine · doi:10.1186/s13073-016-0393-x · Cited by 218 · see citing works
STRUCTURE-FUNCTION OF THE TUMOR SUPPRESSOR BRCA1
Hedgepeth, S. C., Rodriguez, A. M., Snyder, R. R., Hankins, G. D. V., & Boehning, D. F. (2012) · Computational and Structural Biotechnology Journal · doi:10.5936/csbj.201204005 · Cited by 214 · see citing works
Mechanisms of MAPK signalling specificity
Bardwell, L. (2006) · Biochemical Society Transactions · doi:10.1042/bst0340837 · Cited by 213 · see citing works
Xia, L., Huang, W., Bellani, M. A., Seidman, M. M., Wu, K., Fan, D., Nie, Y., Cai, Y., Zhang, Y. W., Yu, L., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.04.005 · Cited by 201 · see citing works
Enhancement of BRCA1 E3 Ubiquitin Ligase Activity through Direct Interaction with the BARD1 Protein
Xia, Y., Pao, G. M., Chen, H.-W., Verma, I. M., & Hunter, T. R. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m204591200 · Cited by 195 · see citing works
Molecular genetics of Bloom's syndrome
Ellis, N. A., & German, J. (1996) · Human Molecular Genetics · doi:10.1093/hmg/5.supplement_1.1457 · Cited by 194 · see citing works
Structural basis for recruitment of BRCA2 by PALB2
Oliver, A. W., Swift, S., Lord, C. J., Ashworth, A., & Pearl, L. H. (2009) · EMBO Reports · doi:10.1038/embor.2009.126 · Cited by 181 · see citing works
Geometric De-noising of Protein-Protein Interaction Networks
Kuchaiev, O., Rašajski, M., Higham, D. J., & Pržulj, N. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000454 · Cited by 180 · see citing works
Michaut, M., Chin, S., Majewski, I. J., Severson, T., Bismeijer, T., de Koning, L., Peeters, J. K., Schouten, P. C., Rueda, O. M., Bosma, A. J., et al. (2016) · Scientific Reports · doi:10.1038/srep18517 · Cited by 169 · see citing works
Romero, O. A., Torres-Diz, M., Pros, E., Savola, S. P., Gómez, A., Morán, S., Sáez, C., Iwakawa, R., Villanueva, A., Montuenga, L. M., et al. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0799 · Cited by 164 · see citing works
Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations
Pahuja, K. B., Nguyen, T. T., Jaiswal, B. S., Prabhash, K., Thaker, T. M., Senger, K., Chaudhuri, S., Kljavin, N. M., Antony, A., Phalke, S., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.09.010 · Cited by 161 · see citing works
A protein interaction landscape of breast cancer
Kim, M., Park, J., Bouhaddou, M., Kim, K., Rojc, A., Modak, M., Soucheray, M., McGregor, M., O’Leary, P. C., Wolf, D. M., et al. (2021) · Science · doi:10.1126/science.abf3066 · Cited by 154 · see citing works
Xiong, P., Zhang, C., Zheng, W., & Zhang, Y. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.11.022 · Cited by 140 · see citing works
Mechanisms of BRCA1–BARD1 nucleosome recognition and ubiquitylation
Hu, Q., Botuyan, M. V., Zhao, D., Cui, G., Mer, E., & Mer, G. (2021) · Nature · doi:10.1038/s41586-021-03716-8 · Cited by 137 · see citing works
MAP3K1: Genomic Alterations in Cancer and Function in Promoting Cell Survival or Apoptosis
Pham, T. T., Angus, S. P., & Johnson, G. L. (2013) · Genes & Cancer · doi:10.1177/1947601913513950 · Cited by 133 · see citing works
Chromatin remodeling in Cancer: A Gateway to regulate gene Transcription
Nair, S. S., & Kumar, R. (2012) · Molecular Oncology · doi:10.1016/j.molonc.2012.09.005 · Cited by 132 · see citing works
The ubiquitin E3 ligase activity of BRCA1 and its biological functions
Wu, W., Koike, A., Takeshita, T., & Ohta, T. (2008) · Cell Division · doi:10.1186/1747-1028-3-1 · Cited by 132 · see citing works
BRCA1 gene: function and deficiency
Takaoka, M., & Miki, Y. (2017) · International Journal of Clinical Oncology · doi:10.1007/s10147-017-1182-2 · Cited by 126 · see citing works
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces
Porta‐Pardo, E., García‐Alonso, L., Hrabe, T., Dopazo, J., & Godzik, A. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004518 · Cited by 126 · see citing works
Littlefield, P., Liu, L., Mysore, V., Shan, Y., Shaw, D. E., & Jura, N. (2014) · Science Signaling · doi:10.1126/scisignal.2005786 · Cited by 126 · see citing works
Becker-Catania, S. G., Chen, G., Hwang, M. J., Wang, Z., Sun, X., Sanal, Ö., Bernatowska, E. A., Chessa, L., Lee, E. Y.-H. P., & Gatti, R. A. (2000) · Molecular Genetics and Metabolism · doi:10.1006/mgme.2000.2998 · Cited by 123 · see citing works
TopBP1: A BRCT-scaffold protein functioning in multiple cellular pathways
Wardlaw, C. P., Carr, A. M., & Oliver, A. W. (2014) · DNA repair · doi:10.1016/j.dnarep.2014.06.004 · Cited by 122 · see citing works
BRCA1 interacts directly with the Fanconi anemia protein FANCA
Folias, A. E. (2002) · Human Molecular Genetics · doi:10.1093/hmg/11.21.2591 · Cited by 118 · see citing works
Cancer Missense Mutations Alter Binding Properties of Proteins and Their Interaction Networks
Nishi, H., Tyagi, M. G., Teng, S., Shoemaker, B. A., Hashimoto, K., Alexov, E. G., Wuchty, S., & Panchenko, A. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066273 · Cited by 117 · see citing works
The value of high quality protein–protein interaction networks for systems biology
Stelzl, U., & Wanker, E. E. (2006) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2006.10.005 · Cited by 115 · see citing works
Unique MAP Kinase binding sites
Akella, R., Moon, T. M., & Goldsmith, E. J. (2008) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2007.09.016 · Cited by 108 · see citing works
Structural Basis for Cell Cycle Checkpoint Control by the BRCA1−CtIP Complex,
Varma, A. K., Brown, R. S., Birrane, G., & Ladias, J. A. A. (2005) · Biochemistry · doi:10.1021/bi0509651 · Cited by 107 · see citing works
Structure of the Fanconi anaemia monoubiquitin ligase complex
Shakeel, S., Rajendra, E., Alcón, P., O’Reilly, F. J., Chorev, D. S., Maslen, S., Degliesposti, G., Russo, C. J., He, S., Hill, C. H., et al. (2019) · Nature · doi:10.1038/s41586-019-1703-4 · Cited by 107 · see citing works
Cancer whole-genome sequencing: present and future
Nakagawa, H., Wardell, C. P., Furuta, M., Taniguchi, H., & Fujimoto, A. (2015) · Oncogene · doi:10.1038/onc.2015.90 · Cited by 106 · see citing works
A comparative study of cancer proteins in the human protein-protein interaction network
Sun, J., & Zhao, Z. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-s3-s5 · Cited by 100 · see citing works
Protein interactions: is seeing believing?
MACKAY, J., SUNDE, M., LOWRY, J., CROSSLEY, M., & MATTHEWS, J. (2007) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2007.09.006 · Cited by 100 · see citing works
OncoVar: an integrated database and analysis platform for oncogenic driver variants in cancers
Wang, T., Ruan, S., Zhao, X., Shi, X., Teng, H., Zhong, J., You, M., Xia, K., Sun, Z. S., & Mao, F. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1033 · Cited by 93 · see citing works
Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces
Engin, H. B., Kreisberg, J. F., & Carter, H. K. (2016) · PLoS ONE · doi:10.1371/journal.pone.0152929 · Cited by 84 · see citing works
Compromised BRCA1–PALB2 interaction is associated with breast cancer risk
Foo, T. K., Tischkowitz, M. D., Simhadri, S. R., Boshari, T., Zayed, N., Burke, K. A., Berman, S. H., Blecua, P., Riaz, N., Huo, Y., et al. (2017) · Oncogene · doi:10.1038/onc.2017.46 · Cited by 84 · see citing works
MAX functions as a tumor suppressor and rewires metabolism in small cell lung cancer
Augert, A., Mathsyaraja, H., Ibrahim, A., Freie, B., Geuenich, M., Cheng, P.-F., Alibeckoff, S. P., Wu, N., Hiatt, J., Basom, R. S., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.04.016 · Cited by 68 · 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
Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era
Porta‐Pardo, E., Valencia, A., & Godzik, A. (2020) · FEBS Letters · doi:10.1002/1873-3468.13781 · Cited by 54 · see citing works
UTRN on chromosome 6q24 is mutated in multiple tumors
Li, Y., Huang, J., Zhao, Y.-L., He, J., Wang, W., Davies, K. E., Nosé, V., & Xiao, S. (2007) · Oncogene · doi:10.1038/sj.onc.1210432 · Cited by 49 · see citing works
Differences in the transactivation domains of p53 family members: a computational study
Mavinahalli, J., Madhumalar, A., Beuerman, R. W., Lane, D. P., & Verma, C. S. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-s1-s5 · Cited by 46 · see citing works
Structure of the FA core ubiquitin ligase closing the ID clamp on DNA
Wang, S., Wang, R., Peralta, C., Yaseen, A., & Pavletich, N. P. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00568-8 · Cited by 44 · see citing works
Fanconi anemia and the underlying causes of genomic instability
Rageul, J., & Kim, H. (2020) · Environmental and Molecular Mutagenesis · doi:10.1002/em.22358 · Cited by 41 · see citing works
Katagiri, T., Fujio, K., Yoshimoto, M., Nomizu, T., Asaishi, K., Abe, R., Tsuchiya, A., Sugano, M., Takai, S., Yoneda, M., et al. (1998) · Journal of Human Genetics · doi:10.1007/s100380050035 · Cited by 38 · see citing works
Arvind, R., Shimamoto, H., Momose, F., Amagasa, T., Omura, K., & Tsuchida, N. (2005) · PubMed · Cited by 32 · see citing works
UTRN inhibits melanoma growth by suppressing p38 and JNK/c-Jun signaling pathways
Zhou, S., Ouyang, W., Zhang, X., Liao, L., Pi, X., Yang, R., Mei, B., Xu, H., Xiang, S., & Li, J. (2021) · Cancer Cell International · doi:10.1186/s12935-021-01768-4 · Cited by 31 · see citing works
Functional and in silico assessment of MAX variants of unknown significance
Comino‐Méndez, I., Leandro-Garcia, L. J., Montoya, G., Inglada‐Pérez, L., de Cubas, A. A., Currás-Freixes, M., Tysoe, C. J., Izatt, L., Letón, R., Gómez-Graña, Á., et al. (2015) · Journal of Molecular Medicine · doi:10.1007/s00109-015-1306-y · Cited by 28 · see citing works
Altered integrin expression patterns shown by microarray in human cutaneous melanoma
Vízkeleti, L., Kiss, T., Koroknai, V., Ecsedi, S., Papp, O., Szász, I., Ádány, R., & Balázs, M. (2017) · Melanoma Research · doi:10.1097/cmr.0000000000000322 · Cited by 27 · see citing works
The DBSAV Database: Predicting Deleteriousness of Single Amino Acid Variations in the Human Proteome
Pei, J., & Grishin, N. V. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.166915 · Cited by 21 · see citing works
Self-citationSpruijt, C. G., Gräwe, C., Kleinendorst, S. C., Baltissen, M. P. A., & Vermeulen, M. (2020) · FEBS Journal · doi:10.1111/febs.15650 · Cited by 19 · see citing works
Hashimoto, K., Wada, K., Matsumoto, K., & Moriya, M. (2015) · DNA repair · doi:10.1016/j.dnarep.2015.09.022 · Cited by 16 · see citing works
Flagged first, then by citations
1 of the 135 references couldn’t be matched to a known paper.
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Burley, S. K., Bhatt, R., Bhikadiya, C., Bi, C., Biester, A., Biswas, P., Bittrich, S., Blaumann, S., Brown, R., Chao, H., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1091 · Cited by 342 · see citing works
Qiu, X., Li, H., Steeg, G. V., & Godzik, A. (2024) · Biomolecules · doi:10.3390/biom14030339 · Cited by 100 · see citing works
Predicting protein-protein interactions in the human proteome
Zhang, J., Humphreys, I. R., Pei, J., Kim, J., Choi, C., Yuan, R., Durham, J., Liu, S., Choi, H.-J., Baek, M., et al. (2025) · Science · doi:10.1126/science.adt1630 · Cited by 87 · see citing works
Self-citationRecent advances in predicting and modeling protein–protein interactions
Durham, J., Zhang, J., Humphreys, I. R., Pei, J., & Cong, Q. (2023) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2023.03.003 · Cited by 80 · see citing works
Self-citationEnhanced Protein-Protein Interaction Discovery via AlphaFold-MultimerPreprint
Kim, A., Hu, Y., Comjean, A., Rodiger, J., Mohr, S. E., & Perrimon, N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.19.580970 · Cited by 76 · see citing works
ModelArchive: A Deposition Database for Computational Macromolecular Structural Models
Tauriello, G., Waterhouse, A. M., Haas, J., Behringer, D., Bienert, S., Garello, T., & Schwede, T. F. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.168996 · Cited by 65 · see citing works
Revolutionizing protein–protein interaction prediction with deep learning
Zhang, J., Durham, J., & Cong, Q. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102775 · Cited by 53 · see citing works
Self-citationProtein interactions in human pathogens revealed through deep learning
Humphreys, I. R., Zhang, J., Baek, M., Wang, Y., Krishnakumar, A., Pei, J., Anishchenko, I. V., Tower, C. A., Jackson, B. A., Warrier, T., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01791-x · Cited by 46 · see citing works
Self-citationMapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens
Walsh, Z. H., Shah, P., Kothapalli, N., Shah, S. B., Nikolényi, G., Brodtman, D. Z., Leuzzi, G., Rogava, M., Mu, M., Ho, P., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02235-x · Cited by 39 · see citing works
Computing the Human InteractomePreprint
Zhang, J., Humphreys, I. R., Pei, J., Kim, J., Choi, C., Yuan, R., Durham, J., Liu, S., Choi, H., Baek, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.01.615885 · Cited by 27 · see citing works
Self-citationDecoding the functional impact of the cancer genome through protein–protein interactions
Fu, H., Mo, X., & Ivanov, A. A. (2025) · Nature reviews. Cancer · doi:10.1038/s41568-024-00784-6 · Cited by 21 · see citing works
Recent progress and future challenges in structure-based protein-protein interaction prediction
Yuan, R., Zhang, J., Zhou, J., & Cong, Q. (2025) · Molecular Therapy · doi:10.1016/j.ymthe.2025.04.003 · Cited by 20 · see citing works
Self-citationWoods, E., Holmes, N., Albaba, S., Evans, I. R., & Balasubramanian, M. (2024) · Clinical Genetics · doi:10.1111/cge.14506 · Cited by 13 · see citing works
Computational analysis of protein–protein interactions of cancer drivers in renal cell carcinoma
Pei, J., Zhang, J., & Cong, Q. (2023) · FEBS Open Bio · doi:10.1002/2211-5463.13732 · Cited by 11 · see citing works
Self-citationDeep learning methods for proteome-scale interaction prediction
Yoon, M. S., Bae, B., Kim, K. H., Park, H., & Baek, M. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102981 · Cited by 5 · see citing works
Histone chaperones as potential epidrug targets against cancer
Malik, S., Kumar, P., Yadav, C. P., Kumar, D., & Kumar, A. (2025) · Nucleosides Nucleotides & Nucleic Acids · doi:10.1080/15257770.2025.2476597 · Cited by 5 · see citing works
Integrative modeling meets deep learning: Recent advances in modeling protein assemblies
Shor, B., & Schneidman‐Duhovny, D. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102841 · Cited by 6 · see citing works
African Swine Fever Virus Protein–Protein Interaction Prediction
Fenster, J. A., Azzinaro, P. A., Dinhobl, M., Borca, M. V., Spinard, E. J., & Gladue, D. P. (2024) · Viruses · doi:10.3390/v16071170 · Cited by 5 · see citing works
Harnessing AlphaFold: Applications in disease understanding, drug discovery, and vaccine design
Kinde, M. Z., Gessese, A. T., Fenta, M. D., Chanie, S. D., & Sisay, T. (2026) · Results in Engineering · doi:10.1016/j.rineng.2026.111095 · Cited by 3 · see citing works
Prediction of protein–protein interactions and co-complex models with deep learning
Zhang, Z., Liu, Y., & Yu, H. (2026) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2026.102703 · Cited by 2 · see citing works
Feng, X., Yang, H., Xu, P., Zhang, S., Britzen‐Laurent, N., Bao, L.-L., Grützmann, R., Krautz, C., & Pilarsky, C. P. (2025) · Cancers · doi:10.3390/cancers17101637 · Cited by 2 · see citing works
Essential and virulence-related protein interactions of pathogens revealed through deep learningPreprint
Humphreys, I. R., Zhang, J., Baek, M., Wang, Y., Krishnakumar, A., Pei, J., Anishchenko, I. V., Tower, C. A., Jackson, B. A., Warrier, T., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.12.589144 · Cited by 2 · see citing works
Self-citationStructural highlights of macromolecular complexes and assemblies
Vallat, B. K., & Berman, H. M. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102773 · Cited by 1 · see citing works
Fu, X., Reglero, C., Swamy, V. S., Loh, J. W., Khiabanian, H., Alberó, R., Forouhar, F., AlQuraishi, M., Ferrando, A. A., & Rabadán, R. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.18.517015 · Cited by 1 · see citing works
Chinami, M. (2025) · Preprints.org · doi:10.20944/preprints202507.2288.v1 · Cited by 1 · see citing works
Walsh, Z. H., Shah, P., Kothapalli, N., Nikolényi, G., Shah, S. B., Leuzzi, G., Mu, M., Ho, P., Abuzaid, S., Brodtman, Z. D., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.13.571465
Caxali, G. H., Aal, M. C. E., Osvaldo, C. W. G., Oliveira, J. S., Bidinotto, L. T., Carvalho, R. F., & Delella, F. K. (2025) · Cell Communication and Signaling · doi:10.1186/s12964-025-02424-4 · Cited by 1 · see citing works
Mohamed, N. M. H. N., Zulkifle, N., & Razak, S. R. A. (2025) · Discover Oncology · doi:10.1007/s12672-025-04232-1
Zhang, J. D. (2026) · Protein Science · doi:10.1002/pro.70551
Self-citationOh, K., Kwon, G.-H., Eom, J.-A., Lee, K. J., Kim, D. J., & Suk, K. T. (2026) · Artificial Cells Nanomedicine and Biotechnology · doi:10.1080/21691401.2026.2694920
- Authors
- Zhang, J., Pei, J., Durham, J., Bos, T., & Cong, Q.
- Affiliations
- The University of Texas Southwestern Medical Center (US)
- Corresponding author
- Cong, Qian
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2022-11-16
- Volume
- 31
- Issue
- 12
- Pages
- e4479-e4479
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- PMC
- PMC9667826
- OpenAlex
- W4306914612
- Cited by
- 31
- References
- 135
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 12 · 2023: 3 · 2022: 2
- FWCI
- 2.20
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Protein Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Cancer Prevention and Research Institute of Texas (RP210041)
- Welch Foundation (I‐2095‐20220331)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Keywords
- protein-protein interaction, somatic missense mutations, coevolution, AlphaFold, protein complex structure prediction, MAP kinase cascade, Fanconi anemia pathway
- MeSH terms
- Humans, Mutation, Neoplasms, Proteins, Mutation, Missense, Protein Interaction Mapping
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.
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