Publications:

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OPUS-Mut: Studying the Effect of Protein Mutation through Side-Chain Modeling.

Journal Of Chemical Theory And Computation

Xu, Gang G; Wang, Qinghua Q; Ma, Jianpeng J

Publication Date: 2023-02-22

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PubMed Link: 36813264

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• ct2c00847.pdf

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Sequence Properties of An Intramolecular Interaction That Inhibits p53 DNA Binding.

Biomolecules

Gregory, Emily E; Daughdrill, Gary W GW

Publication Date: 2022-10-25

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PubMed Link: 36358908

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• biomolecules-12-01558.pdf

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Genomic landscape, immune characteristics and prognostic mutation signature of cervical cancer in China.

Bmc Medical Genomics

Liu, Jing J; Li, Zirong Z; Lu, Ting T; Pan, Junping J; Li, Li L; Song, Yanwen Y; Hu, Dan D; Zhuo, Yanhong Y; Chen, Ying Y; Xu, Qin Q

Publication Date: 2022-11-04

Variant appearance in text: TP53: 715A>T; N239Y

PubMed Link: 36333792

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• 12920_2022_1376_MOESM1_ESM.xlsx, sheet 1

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A small molecule reacts with the p53 somatic mutant Y220C to rescue wild-type thermal stability.

Cancer Discovery

Guiley, Keelan Z KZ; Shokat, Kevan M KM

Publication Date: 2022-10-05

Variant appearance in text: p53: N239Y

PubMed Link: 36197521

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• Main text
• 56.pdf

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CTCF DNA-binding domain undergoes dynamic and selective protein-protein interactions.

Iscience

Zhou, Rong R; Tian, Kai K; Huang, Jie J; Duan, Wenjia W; Fu, Hongye H; Feng, Ying Y; Wang, Hui H; Jiang, Yongpeng Y; Li, Yuanjun Y; Wang, Rui R; Hu, Jiazhi J; Ma, Hanhui H; Qi, Zhi Z; Ji, Xiong X

Publication Date: 2022-09-16

Variant appearance in text: p53: 715A>T

PubMed Link: 36117989

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• mmc4.xlsx, sheet 1

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Insights into Allosteric Mechanisms of the Lung-Enriched p53 Mutants V157F and R158L.

International Journal Of Molecular Sciences

Lei, Jiangtao J; Li, Xuanyao X; Cai, Mengqiang M; Guo, Tianjing T; Lin, Dongdong D; Deng, Xiaohua X; Li, Yin Y

Publication Date: 2022-09-03

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PubMed Link: 36077492

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• ijms-23-10100.pdf

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Mechanistic insights into global suppressors of protein folding defects.

Plos Genetics

Chattopadhyay, Gopinath G; Bhowmick, Jayantika J; Manjunath, Kavyashree K; Ahmed, Shahbaz S; Goyal, Parveen P; Varadarajan, Raghavan R

Publication Date: 2022-08

Variant appearance in text: p53: N239Y

PubMed Link: 36037221

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• pgen.1010334.pdf

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Construction and validation of an immunoediting-based optimized neoantigen load (ioTNL) model to predict the response and prognosis of immune checkpoint therapy in various cancers.

Aging

Su, Xiaofan X; Jin, Haoxuan H; Wang, Jiaqian J; Lu, Huiping H; Gu, Tiantian T; Gao, Zhibo Z; Li, Manxiang M

Publication Date: 2022-05-25

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PubMed Link: 35613927

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• aging-14-204101-s004.xlsx, sheet 1

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Evolutionary history of the p53 family DNA-binding domain: insights from an Alvinella pompejana homolog.

Cell Death & Disease

Zhang, Qiang Q; Balourdas, Dimitrios-Ilias DI; Baron, Bruno B; Senitzki, Alon A; Haran, Tali E TE; Wiman, Klas G KG; Soussi, Thierry T; Joerger, Andreas C AC

Publication Date: 2022-03-07

Variant appearance in text: p53: N239Y

PubMed Link: 35256607

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• Main text
• 41419_2022_Article_4653.pdf

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Targeted Therapy of Papillary Thyroid Cancer: A Comprehensive Genomic Analysis.

Frontiers In Endocrinology

Hescheler, Daniel A DA; Riemann, Burkhard B; Hartmann, Milan J M MJM; Michel, Maximilian M; Faust, Michael M; Bruns, Christiane J CJ; Alakus, Hakan H; Chiapponi, Costanza C

Publication Date: 2021

Variant appearance in text: TP53: N239Y

PubMed Link: 34630336

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• Table_1.xlsx, sheet 2

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Structural and Drug Targeting Insights on Mutant p53.

Cancers

Gomes, Ana Sara AS; Ramos, Helena H; Inga, Alberto A; Sousa, Emília E; Saraiva, Lucília L

Publication Date: 2021-07-03

Variant appearance in text: p53: N239Y

PubMed Link: 34283062

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• Main text
• cancers-13-03344.pdf

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Mutation profile and immunoscore signature in thymic carcinomas: An exploratory study and review of the literature.

Thoracic Cancer

Asselta, Rosanna R; Di Tommaso, Luca L; Perrino, Matteo M; Destro, Annarita A; Giordano, Laura L; Cardamone, Giulia G; Rubino, Luca L; Santoro, Armando A; Duga, Stefano S; Zucali, Paolo Andrea PA

Publication Date: 2021-05

Variant appearance in text: TP53: 715A>T; N239Y

PubMed Link: 33704917

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• TCA-12-1271-s003.xls, sheet 1

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A phosphorylation-dependent switch in the disordered p53 transactivation domain regulates DNA binding.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Sun, Xun X; Dyson, H Jane HJ; Wright, Peter E PE

Publication Date: 2021-01-05

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PubMed Link: 33443163

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Novel bioinformatic classification system for genetic signatures identification in diffuse large B-cell lymphoma.

Bmc Cancer

Zhang, Wei W; Yang, Li L; Guan, Yu' Qi YQ; Shen, Ke' Feng KF; Zhang, Mei' Lan ML; Cai, Hao' Dong HD; Wang, Jia' Chen JC; Wang, Ying Y; Huang, Liang L; Cao, Yang Y; Wang, Na N; Tan, Xiao' Hong XH; Young, Ken He KH; Xiao, Min M; Zhou, Jian' Feng JF

Publication Date: 2020-07-31

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PubMed Link: 32736575

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• 12885_2020_7198_MOESM5_ESM.xlsx, sheet 1

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Tumorigenic p53 mutants undergo common structural disruptions including conversion to α-sheet structure.

Protein Science : A Publication Of The Protein Society

Bromley, Dennis D; Daggett, Valerie V

Publication Date: 2020-09

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PubMed Link: 32715544

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Defining relative mutational difficulty to understand cancer formation.

Cell Discovery

Shan, Lin L; Yu, Jiao J; He, Zhengjin Z; Chen, Shishuang S; Liu, Mingxian M; Ding, Hongyu H; Xu, Liang L; Zhao, Jie J; Yang, Ailing A; Jiang, Hai H

Publication Date: 2020

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PubMed Link: 32704382

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• 41421_2020_177_MOESM5_ESM.xlsx, sheet 1
• 41421_2020_177_MOESM6_ESM.xlsx, sheet 1

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Inhibition of p53 DNA binding by a small molecule protects mice from radiation toxicity.

Oncogene

Li, Qingliang Q; Karim, Rezaul M RM; Cheng, Mo M; Das, Mousumi M; Chen, Lihong L; Zhang, Chen C; Lawrence, Harshani R HR; Daughdrill, Gary W GW; Schonbrunn, Ernst E; Ji, Haitao H; Chen, Jiandong J

Publication Date: 2020-07

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PubMed Link: 32555331

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Identification of targeted therapy options for gastric adenocarcinoma by comprehensive analysis of genomic data.

Gastric Cancer : Official Journal Of The International Gastric Cancer Association And The Japanese Gastric Cancer Association

Hescheler, Daniel A DA; Plum, Patrick S PS; Zander, Thomas T; Quaas, Alexander A; Korenkov, Michael M; Gassa, Asmae A; Michel, Maximilian M; Bruns, Christiane J CJ; Alakus, Hakan H

Publication Date: 2020-07

Variant appearance in text: TP53: N239Y

PubMed Link: 32107691

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• 10120_2020_1045_MOESM1_ESM.xlsx, sheet 12

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Targeting Cavity-Creating p53 Cancer Mutations with Small-Molecule Stabilizers: the Y220X Paradigm.

Acs Chemical Biology

Bauer, Matthias R MR; Krämer, Andreas A; Settanni, Giovanni G; Jones, Rhiannon N RN; Ni, Xiaomin X; Khan Tareque, Raysa R; Fersht, Alan R AR; Spencer, John J; Joerger, Andreas C AC

Publication Date: 2020-03-20

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PubMed Link: 31990523

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• Main text
• cb9b00748_si_001.pdf
• cb9b00748.pdf

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White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer.

Nature Communications

Leal, Alessandro A; van Grieken, Nicole C T NCT; Palsgrove, Doreen N DN; Phallen, Jillian J; Medina, Jamie E JE; Hruban, Carolyn C; Broeckaert, Mark A M MAM; Anagnostou, Valsamo V; Adleff, Vilmos V; Bruhm, Daniel C DC; Canzoniero, Jenna V JV; Fiksel, Jacob J; Nordsmark, Marianne M; Warmerdam, Fabienne A R M FARM; Verheul, Henk M W HMW; van Spronsen, Dick Johan DJ; Beerepoot, Laurens V LV; Geenen, Maud M MM; Portielje, Johanneke E A JEA; Jansen, Edwin P M EPM; van Sandick, Johanna J; Meershoek-Klein Kranenbarg, Elma E; van Laarhoven, Hanneke W M HWM; van der Peet, Donald L DL; van de Velde, Cornelis J H CJH; Verheij, Marcel M; Fijneman, Remond R; Scharpf, Robert B RB; Meijer, Gerrit A GA; Cats, Annemieke A; Velculescu, Victor E VE

Publication Date: 2020-01-27

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PubMed Link: 31988276

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• 41467_2020_14310_MOESM6_ESM.xlsx, sheet 6
• 41467_2020_14310_MOESM6_ESM.xlsx, sheet 8
• 41467_2020_14310_MOESM10_ESM.xlsx, sheet 1
• 41467_2020_14310_MOESM8_ESM.xlsx, sheet 1

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A structure-guided molecular chaperone approach for restoring the transcriptional activity of the p53 cancer mutant Y220C.

Future Medicinal Chemistry

Bauer, Matthias R MR; Jones, Rhiannon N RN; Tareque, Raysa K RK; Springett, Bradley B; Dingler, Felix A FA; Verduci, Lorena L; Patel, Ketan J KJ; Fersht, Alan R AR; Joerger, Andreas C AC; Spencer, John J

Publication Date: 2019-10

Variant appearance in text: p53: N239Y

PubMed Link: 31633398

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• fmc-11-2491.pdf

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Functional Rescue of Cataract-Causing αA-G98R-Crystallin by Targeted Compensatory Suppressor Mutations in Human αA-Crystallin.

Biochemistry

Phadte, Ashutosh S AS; Mahalingam, Sundararajan S; Santhoshkumar, Puttur P; Sharma, Krishna K KK

Publication Date: 2019-10-08

Variant appearance in text: p53: N239Y

PubMed Link: 31523965

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Finding driver mutations in cancer: Elucidating the role of background mutational processes.

Plos Computational Biology

Brown, Anna-Leigh AL; Li, Minghui M; Goncearenco, Alexander A; Panchenko, Anna R AR

Publication Date: 2019-04

Variant appearance in text: TP53: N239Y

PubMed Link: 31034466

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• pcbi.1006981.s010.xlsx, sheet 1

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Simulations of mutant p53 DNA binding domains reveal a novel druggable pocket.

Nucleic Acids Research

Pradhan, Mohan R MR; Siau, Jia Wei JW; Kannan, Srinivasaraghavan S; Nguyen, Minh N MN; Ouaray, Zohra Z; Kwoh, Chee Keong CK; Lane, David P DP; Ghadessy, Farid F; Verma, Chandra S CS

Publication Date: 2019-02-28

Variant appearance in text: p53: N239Y

PubMed Link: 30649466

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• Main text
• gky1314.pdf

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Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Krois, Alexander S AS; Dyson, H Jane HJ; Wright, Peter E PE

Publication Date: 2018-11-27

Variant appearance in text: p53: N239Y

PubMed Link: 30420502

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Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

Nature Communications

Zhu, Yafeng Y; Orre, Lukas M LM; Johansson, Henrik J HJ; Huss, Mikael M; Boekel, Jorrit J; Vesterlund, Mattias M; Fernandez-Woodbridge, Alejandro A; Branca, Rui M M RMM; Lehtiö, Janne J

Publication Date: 2018-03-02

Variant appearance in text: TP53: 715A>T; N239Y

PubMed Link: 29500430

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• 41467_2018_3311_MOESM5_ESM.xlsx, sheet 1

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Effects of Y361-auto-phosphorylation on structural plasticity of the HIPK2 kinase domain.

Protein Science : A Publication Of The Protein Society

Scaglione, Antonella A; Monteonofrio, Laura L; Parisi, Giacomo G; Cecchetti, Cristina C; Siepi, Francesca F; Rinaldo, Cinzia C; Giorgi, Alessandra A; Verzili, Daniela D; Zamparelli, Carlotta C; Savino, Carmelinda C; Soddu, Silvia S; Vallone, Beatrice B; Montemiglio, Linda Celeste LC

Publication Date: 2018-03

Variant appearance in text: p53: N239Y

PubMed Link: 29277937

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Insights into the Effect of the G245S Single Point Mutation on the Structure of p53 and the Binding of the Protein to DNA.

Molecules (Basel, Switzerland)

Lepre, Marco Gaetano MG; Omar, Sara Ibrahim SI; Grasso, Gianvito G; Morbiducci, Umberto U; Deriu, Marco Agostino MA; Tuszynski, Jack A JA

Publication Date: 2017-08-16

Variant appearance in text: p53: N239Y

PubMed Link: 28813011

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Pan-urologic cancer genomic subtypes that transcend tissue of origin.

Nature Communications

Chen, Fengju F; Zhang, Yiqun Y; Bossé, Dominick D; Lalani, Aly-Khan A AA; Hakimi, A Ari AA; Hsieh, James J JJ; Choueiri, Toni K TK; Gibbons, Don L DL; Ittmann, Michael M; Creighton, Chad J CJ

Publication Date: 2017-08-04

Variant appearance in text: TP53: 715A>T; N239Y

PubMed Link: 28775315

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• 41467_2017_289_MOESM7_ESM.xlsx, sheet 1

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Structures of closed and open conformations of dimeric human ATM.

Science Advances

Baretić, Domagoj D; Pollard, Hannah K HK; Fisher, David I DI; Johnson, Christopher M CM; Santhanam, Balaji B; Truman, Caroline M CM; Kouba, Tomas T; Fersht, Alan R AR; Phillips, Christopher C; Williams, Roger L RL

Publication Date: 2017-05

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PubMed Link: 28508083

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• Main text
• 1700933.pdf

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The mutational status of p53 can influence its recognition by human T-cells.

Oncoimmunology

Shamalov, Katerina K; Levy, Shlomo N SN; Horovitz-Fried, Miryam M; Cohen, Cyrille J CJ

Publication Date: 2017

Variant appearance in text: p53: N239Y

PubMed Link: 28507791

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Design of a molecular support for cryo-EM structure determination.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Martin, Thomas G TG; Bharat, Tanmay A M TA; Joerger, Andreas C AC; Bai, Xiao-Chen XC; Praetorius, Florian F; Fersht, Alan R AR; Dietz, Hendrik H; Scheres, Sjors H W SH

Publication Date: 2016-11-22

Variant appearance in text: p53: N239Y

PubMed Link: 27821763

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Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds.

Scientific Reports

Cino, Elio A EA; Soares, Iaci N IN; Pedrote, Murilo M MM; de Oliveira, Guilherme A P GA; Silva, Jerson L JL

Publication Date: 2016-09-07

Variant appearance in text: p53: N239Y

PubMed Link: 27600721

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• Main text
• srep32535.pdf

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iFish: predicting the pathogenicity of human nonsynonymous variants using gene-specific/family-specific attributes and classifiers.

Scientific Reports

Wang, Meng M; Wei, Liping L

Publication Date: 2016-08-16

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PubMed Link: 27527004

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• srep31321-s5.xls, sheet 1

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An in silico algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein.

Protein Engineering, Design & Selection : Peds

Bromley, Dennis D; Bauer, Matthias R MR; Fersht, Alan R AR; Daggett, Valerie V

Publication Date: 2016-09

Variant appearance in text: p53: N239Y

PubMed Link: 27503952

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GESPA: classifying nsSNPs to predict disease association.

Bmc Bioinformatics

Khurana, Jay K JK; Reeder, Jay E JE; Shrimpton, Antony E AE; Thakar, Juilee J

Publication Date: 2015-07-25

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PubMed Link: 26206375

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• 12859_2015_673_MOESM1_ESM.xls, sheet 1

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Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology.

Protein Science : A Publication Of The Protein Society

Sinz, Andrea A; Arlt, Christian C; Chorev, Dror D; Sharon, Michal M

Publication Date: 2015-08

Variant appearance in text: p53: N239Y

PubMed Link: 25970732

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Propagation of aggregated p53: Cross-reaction and coaggregation vs. seeding.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Wang, GuoZhen G; Fersht, Alan R AR

Publication Date: 2015-02-24

Variant appearance in text: p53: N239Y

PubMed Link: 25675527

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Mechanism of initiation of aggregation of p53 revealed by Φ-value analysis.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Wang, GuoZhen G; Fersht, Alan R AR

Publication Date: 2015-02-24

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PubMed Link: 25675526

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Oxidation of p53 through DNA charge transport involves a network of disulfides within the DNA-binding domain.

Biochemistry

Schaefer, Kathryn N KN; Geil, Wendy M WM; Sweredoski, Michael J MJ; Moradian, Annie A; Hess, Sonja S; Barton, Jacqueline K JK

Publication Date: 2015-01-27

Variant appearance in text: p53: N239Y

PubMed Link: 25584637

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• Main text
• bi501424v_si_001.pdf
• bi501424v.pdf

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Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations.

Genome Biology

Martelotto, Luciano G LG; Ng, Charlotte Ky CK; De Filippo, Maria R MR; Zhang, Yan Y; Piscuoglio, Salvatore S; Lim, Raymond S RS; Shen, Ronglai R; Norton, Larry L; Reis-Filho, Jorge S JS; Weigelt, Britta B

Publication Date: 2014-10-28

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PubMed Link: 25348012

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• 13059_2014_484_MOESM2_ESM.xlsx, sheet 1

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Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue.

Acta Crystallographica. Section D, Biological Crystallography

Wallentine, Brad D BD; Wang, Ying Y; Tretyachenko-Ladokhina, Vira V; Tan, Martha M; Senear, Donald F DF; Luecke, Hartmut H

Publication Date: 2013-10

Variant appearance in text: p53: N239Y

PubMed Link: 24100332

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A novel p53 mutant found in iatrogenic urothelial cancers is dysfunctional and can be rescued by a second-site global suppressor mutation.

The Journal Of Biological Chemistry

Odell, Adam F AF; Odell, Luke R LR; Askham, Jon M JM; Alogheli, Hiba H; Ponnambalam, Sreenivasan S; Hollstein, Monica M

Publication Date: 2013-06-07

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PubMed Link: 23612969

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Molecular basis for modulation of the p53 target selectivity by KLF4.

Plos One

Brandt, Tobias T; Townsley, Fiona M FM; Teufel, Daniel P DP; Freund, Stefan M V SM; Veprintsev, Dmitry B DB

Publication Date: 2012

Variant appearance in text: p53: N239Y

PubMed Link: 23118962

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Stability of p53 homologs.

Plos One

Brandt, Tobias T; Kaar, Joel L JL; Fersht, Alan R AR; Veprintsev, Dmitry B DB

Publication Date: 2012

Variant appearance in text: p53: N239Y

PubMed Link: 23112865

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Domain-domain interactions in full-length p53 and a specific DNA complex probed by methyl NMR spectroscopy.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Bista, Michal M; Freund, Stefan M SM; Fersht, Alan R AR

Publication Date: 2012-09-25

Variant appearance in text: p53: N239Y

PubMed Link: 22972749

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Identification & Characterization of lactobacillus salavarius bacteriocins and its relevance in cancer therapeutics.

Bioinformation

Shaikh, Faraz F; Abhinand, Pa P; Ragunath, Pk P

Publication Date: 2012

Variant appearance in text: p53: N239Y

PubMed Link: 22829737

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Specific recognition of p53 tetramers by peptides derived from p53 interacting proteins.

Plos One

Gabizon, Ronen R; Brandt, Tobias T; Sukenik, Shahar S; Lahav, Noa N; Lebendiker, Mario M; Shalev, Deborah E DE; Veprintsev, Dmitry D; Friedler, Assaf A

Publication Date: 2012

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PubMed Link: 22693587

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Analyzing effects of naturally occurring missense mutations.

Computational And Mathematical Methods In Medicine

Zhang, Zhe Z; Miteva, Maria A MA; Wang, Lin L; Alexov, Emil E

Publication Date: 2012

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PubMed Link: 22577471

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