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For: Li M, Kales SC, Ma K, Shoemaker BA, Crespo-Barreto J, Cangelosi AL, Lipkowitz S, Panchenko AR. Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation. Cancer Res 2015;76:561-71. [PMID: 26676746 DOI: 10.1158/0008-5472.can-14-3812] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 11/22/2015] [Indexed: 12/19/2022]
Number Cited by Other Article(s)
1
Wang S, Tang H, Shan P, Wu Z, Zuo L. ProS-GNN: Predicting effects of mutations on protein stability using graph neural networks. Comput Biol Chem 2023;107:107952. [PMID: 37643501 DOI: 10.1016/j.compbiolchem.2023.107952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
2
Fang J. Predicting thermostability difference between cellular protein orthologs. Bioinformatics 2023;39:btad504. [PMID: 37572303 PMCID: PMC10457660 DOI: 10.1093/bioinformatics/btad504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/02/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023]  Open
3
Ostroverkhova D, Przytycka TM, Panchenko AR. Cancer driver mutations: predictions and reality. Trends Mol Med 2023:S1471-4914(23)00067-9. [PMID: 37076339 DOI: 10.1016/j.molmed.2023.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
4
Role of CBL Mutations in Cancer and Non-Malignant Phenotype. Cancers (Basel) 2022;14:cancers14030839. [PMID: 35159106 PMCID: PMC8833995 DOI: 10.3390/cancers14030839] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 12/30/2022]  Open
5
Norris GA, Tsai ACH, Schneider KW, Wu YH, Caulfield T, Green AL. A novel, germline, deactivating CBL variant p.L493F alters domain orientation and is associated with multiple childhood cancers. Cancer Genet 2021;254-255:18-24. [PMID: 33550024 DOI: 10.1016/j.cancergen.2021.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/26/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
6
Tan ZW, Guarnera E, Tee WV, Berezovsky IN. AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations. Nucleic Acids Res 2020;48:W116-W124. [PMID: 32392302 PMCID: PMC7319554 DOI: 10.1093/nar/gkaa338] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/09/2020] [Accepted: 04/22/2020] [Indexed: 12/21/2022]  Open
7
Insights into changes in binding affinity caused by disease mutations in protein-protein complexes. Comput Biol Med 2020;123:103829. [DOI: 10.1016/j.compbiomed.2020.103829] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 01/11/2023]
8
Allosteric drugs and mutations: chances, challenges, and necessity. Curr Opin Struct Biol 2020;62:149-157. [DOI: 10.1016/j.sbi.2020.01.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022]
9
Zhang N, Chen Y, Lu H, Zhao F, Alvarez RV, Goncearenco A, Panchenko AR, Li M. MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions. iScience 2020;23:100939. [PMID: 32169820 PMCID: PMC7068639 DOI: 10.1016/j.isci.2020.100939] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/21/2019] [Accepted: 02/20/2020] [Indexed: 01/17/2023]  Open
10
Somarelli JA, Gardner H, Cannataro VL, Gunady EF, Boddy AM, Johnson NA, Fisk JN, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, DeGregori J, Townsend JP. Molecular Biology and Evolution of Cancer: From Discovery to Action. Mol Biol Evol 2020;37:320-326. [PMID: 31642480 PMCID: PMC6993850 DOI: 10.1093/molbev/msz242] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
11
de Oliveira VM, Caetano DLZ, da Silva FB, Mouro PR, de Oliveira AB, de Carvalho SJ, Leite VBP. pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study. J Chem Theory Comput 2020;16:765-772. [PMID: 31756296 DOI: 10.1021/acs.jctc.9b00894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
12
Nussinov R, Tsai C, Jang H. Autoinhibition can identify rare driver mutations and advise pharmacology. FASEB J 2019;34:16-29. [DOI: 10.1096/fj.201901341r] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/18/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022]
13
Tee WV, Guarnera E, Berezovsky IN. On the Allosteric Effect of nsSNPs and the Emerging Importance of Allosteric Polymorphism. J Mol Biol 2019;431:3933-3942. [PMID: 31306666 DOI: 10.1016/j.jmb.2019.07.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/11/2019] [Accepted: 07/04/2019] [Indexed: 12/19/2022]
14
Fang J. A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. Brief Bioinform 2019;21:1285-1292. [PMID: 31273374 DOI: 10.1093/bib/bbz071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 01/02/2023]  Open
15
Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN. Mutational signatures and mutable motifs in cancer genomes. Brief Bioinform 2019;19:1085-1101. [PMID: 28498882 DOI: 10.1093/bib/bbx049] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 12/22/2022]  Open
16
Goncearenco A, Rager SL, Li M, Sang QX, Rogozin IB, Panchenko AR. Exploring background mutational processes to decipher cancer genetic heterogeneity. Nucleic Acids Res 2019;45:W514-W522. [PMID: 28472504 PMCID: PMC5793731 DOI: 10.1093/nar/gkx367] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/21/2017] [Indexed: 01/08/2023]  Open
17
On the perturbation nature of allostery: sites, mutations, and signal modulation. Curr Opin Struct Biol 2019;56:18-27. [DOI: 10.1016/j.sbi.2018.10.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/27/2018] [Accepted: 10/30/2018] [Indexed: 10/27/2022]
18
Tsuda Y, Hirata M, Katayama K, Motoi T, Matsubara D, Oda Y, Fujita M, Kobayashi H, Kawano H, Nishida Y, Sakai T, Okuma T, Goto T, Ogura K, Kawai A, Ae K, Anazawa U, Suehara Y, Iwata S, Miyano S, Imoto S, Shibata T, Nakagawa H, Yamaguchi R, Tanaka S, Matsuda K. Massively parallel sequencing of tenosynovial giant cell tumors reveals novel CSF1 fusion transcripts and novel somatic CBL mutations. Int J Cancer 2019;145:3276-3284. [PMID: 31107544 DOI: 10.1002/ijc.32421] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/10/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2022]
19
Brown AL, Li M, Goncearenco A, Panchenko AR. Finding driver mutations in cancer: Elucidating the role of background mutational processes. PLoS Comput Biol 2019;15:e1006981. [PMID: 31034466 PMCID: PMC6508748 DOI: 10.1371/journal.pcbi.1006981] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/09/2019] [Accepted: 03/28/2019] [Indexed: 01/22/2023]  Open
20
Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput Biol 2019;15:e1006658. [PMID: 30921324 PMCID: PMC6438456 DOI: 10.1371/journal.pcbi.1006658] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
21
PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions. PLoS Comput Biol 2018;14:e1006615. [PMID: 30533007 PMCID: PMC6303081 DOI: 10.1371/journal.pcbi.1006615] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/21/2018] [Accepted: 11/01/2018] [Indexed: 01/01/2023]  Open
22
Computational Approaches to Prioritize Cancer Driver Missense Mutations. Int J Mol Sci 2018;19:ijms19072113. [PMID: 30037003 PMCID: PMC6073793 DOI: 10.3390/ijms19072113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 12/31/2022]  Open
23
Trade-offs with stability modulate innate and mutationally acquired drug resistance in bacterial dihydrofolate reductase enzymes. Biochem J 2018;475:2107-2125. [PMID: 29871875 DOI: 10.1042/bcj20180249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 01/30/2023]
24
Cheng F, Hong H, Yang S, Wei Y. Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era. Brief Bioinform 2017;18:682-697. [PMID: 27296652 DOI: 10.1093/bib/bbw051] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 12/12/2022]  Open
25
Li M, Goncearenco A, Panchenko AR. Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. Methods Mol Biol 2017;1550:235-260. [PMID: 28188534 PMCID: PMC5388446 DOI: 10.1007/978-1-4939-6747-6_17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
26
Lack of Correlation between Aberrant p16, RAR-β2, TIMP3, ERCC1, and BRCA1 Protein Expression and Promoter Methylation in Squamous Cell Carcinoma Accompanying Candida albicans-Induced Inflammation. PLoS One 2016;11:e0159090. [PMID: 27410681 PMCID: PMC4943641 DOI: 10.1371/journal.pone.0159090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/27/2016] [Indexed: 02/06/2023]  Open
27
Li M, Simonetti FL, Goncearenco A, Panchenko AR. MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions. Nucleic Acids Res 2016;44:W494-501. [PMID: 27150810 PMCID: PMC4987923 DOI: 10.1093/nar/gkw374] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/23/2016] [Indexed: 11/13/2022]  Open
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