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Items: 1 to 50 of 108

1.

A Multireporter Bacterial 2-Hybrid Assay for the High-Throughput and Dynamic Assay of PDZ Domain-Peptide Interactions.

Ichikawa DM, Corbi-Verge C, Shen MJ, Snider J, Wong V, Stagljar I, Kim PM, Noyes MB.

ACS Synth Biol. 2019 May 17;8(5):918-928. doi: 10.1021/acssynbio.8b00499. Epub 2019 Apr 18.

PMID:
30969105
2.

Piezo1 incorporates mechanical force signals into the genetic program that governs lymphatic valve development and maintenance.

Choi D, Park E, Jung E, Cha B, Lee S, Yu J, Kim PM, Lee S, Hong YJ, Koh CJ, Cho CW, Wu Y, Li Jeon N, Wong AK, Shin L, Kumar SR, Bermejo-Moreno I, Srinivasan RS, Cho IT, Hong YK.

JCI Insight. 2019 Mar 7;4(5). pii: 125068. doi: 10.1172/jci.insight.125068. eCollection 2019 Mar 7.

3.

An Unusual Case of a Fibular Sesamoid Phalangeal Ligament Tear Caused By Chronic Trauma.

Levi M, Green JI, Kim PM, Saxena A.

J Am Podiatr Med Assoc. 2019 Mar;109(2):162-165. doi: 10.7547/18-052. Epub 2019 Jan 12.

PMID:
30638030
4.

Rapid and accurate structure-based therapeutic peptide design using GPU accelerated thermodynamic integration.

Garton M, Corbi-Verge C, Hu Y, Nim S, Tarasova N, Sherborne B, Kim PM.

Proteins. 2019 Mar;87(3):236-244. doi: 10.1002/prot.25644. Epub 2019 Jan 4.

PMID:
30520126
5.

Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores.

Ben-David M, Huang H, Sun MGF, Corbi-Verge C, Petsalaki E, Liu K, Gfeller D, Garg P, Tempel W, Sochirca I, Shifman JM, Davidson A, Min J, Kim PM, Sidhu SS.

J Mol Biol. 2019 Jan 18;431(2):336-350. doi: 10.1016/j.jmb.2018.11.018. Epub 2018 Nov 22.

PMID:
30471255
6.

A PxL motif promotes timely cell cycle substrate dephosphorylation by the Cdc14 phosphatase.

Kataria M, Mouilleron S, Seo MH, Corbi-Verge C, Kim PM, Uhlmann F.

Nat Struct Mol Biol. 2018 Dec;25(12):1093-1102. doi: 10.1038/s41594-018-0152-3. Epub 2018 Nov 19.

7.

Predicting the Effect of Mutations on Protein Folding and Protein-Protein Interactions.

Strokach A, Corbi-Verge C, Teyra J, Kim PM.

Methods Mol Biol. 2019;1851:1-17. doi: 10.1007/978-1-4939-8736-8_1.

PMID:
30298389
8.

Exosomes as a Communication Tool Between the Lymphatic System and Bladder Cancer.

Park RJ, Hong YJ, Wu Y, Kim PM, Hong YK.

Int Neurourol J. 2018 Sep;22(3):220-224. doi: 10.5213/inj.1836186.093. Epub 2018 Sep 28. No abstract available.

9.

Endothelial lineage-specific interaction of Mycobacterium tuberculosis with the blood and lymphatic systems.

Kim PM, Lee JJ, Choi D, Eoh H, Hong YK.

Tuberculosis (Edinb). 2018 Jul;111:1-7. doi: 10.1016/j.tube.2018.04.009. Epub 2018 May 4. Review.

PMID:
30029892
10.

The present and the future of motif-mediated protein-protein interactions.

Seo MH, Kim PM.

Curr Opin Struct Biol. 2018 Jun;50:162-170. doi: 10.1016/j.sbi.2018.04.005. Epub 2018 May 3. Review.

PMID:
29730529
11.

Dimethyl fumarate targets GAPDH and aerobic glycolysis to modulate immunity.

Kornberg MD, Bhargava P, Kim PM, Putluri V, Snowman AM, Putluri N, Calabresi PA, Snyder SH.

Science. 2018 Apr 27;360(6387):449-453. doi: 10.1126/science.aan4665. Epub 2018 Mar 29.

12.

Bryostatin-1 alleviates experimental multiple sclerosis.

Kornberg MD, Smith MD, Shirazi HA, Calabresi PA, Snyder SH, Kim PM.

Proc Natl Acad Sci U S A. 2018 Feb 27;115(9):2186-2191. doi: 10.1073/pnas.1719902115. Epub 2018 Feb 12.

13.

Method to generate highly stable D-amino acid analogs of bioactive helical peptides using a mirror image of the entire PDB.

Garton M, Nim S, Stone TA, Wang KE, Deber CM, Kim PM.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):1505-1510. doi: 10.1073/pnas.1711837115. Epub 2018 Jan 29.

14.

The Chemical Fluctuation Theorem governing gene expression.

Park SJ, Song S, Yang GS, Kim PM, Yoon S, Kim JH, Sung J.

Nat Commun. 2018 Jan 19;9(1):297. doi: 10.1038/s41467-017-02737-0.

15.

A computational approach for designing D-proteins with non-canonical amino acid optimised binding affinity.

Garton M, Sayadi M, Kim PM.

PLoS One. 2017 Nov 6;12(11):e0187524. doi: 10.1371/journal.pone.0187524. eCollection 2017.

16.

Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities.

Teyra J, Huang H, Jain S, Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, Bader GD, Sidhu SS.

Structure. 2017 Oct 3;25(10):1598-1610.e3. doi: 10.1016/j.str.2017.07.017. Epub 2017 Sep 7.

17.

Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding.

Najafabadi HS, Garton M, Weirauch MT, Mnaimneh S, Yang A, Kim PM, Hughes TR.

Genome Biol. 2017 Sep 6;18(1):167. doi: 10.1186/s13059-017-1287-y.

18.

Data driven flexible backbone protein design.

Sun MGF, Kim PM.

PLoS Comput Biol. 2017 Aug 24;13(8):e1005722. doi: 10.1371/journal.pcbi.1005722. eCollection 2017 Aug.

19.

Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome.

Davey NE, Seo MH, Yadav VK, Jeon J, Nim S, Krystkowiak I, Blikstad C, Dong D, Markova N, Kim PM, Ivarsson Y.

FEBS J. 2017 Feb;284(3):485-498. doi: 10.1111/febs.13995. Epub 2017 Jan 18.

20.
21.

Strategies to Develop Inhibitors of Motif-Mediated Protein-Protein Interactions as Drug Leads.

Corbi-Verge C, Garton M, Nim S, Kim PM.

Annu Rev Pharmacol Toxicol. 2017 Jan 6;57:39-60. doi: 10.1146/annurev-pharmtox-010716-104805. Epub 2016 Sep 8. Review.

PMID:
27618737
22.

Protein engineering by highly parallel screening of computationally designed variants.

Sun MG, Seo MH, Nim S, Corbi-Verge C, Kim PM.

Sci Adv. 2016 Jul 20;2(7):e1600692. doi: 10.1126/sciadv.1600692. eCollection 2016 Jul.

23.

PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies.

Jeon J, Arnold R, Singh F, Teyra J, Braun T, Kim PM.

BMC Bioinformatics. 2016 Apr 1;17:150. doi: 10.1186/s12859-016-1001-1.

24.

Motif mediated protein-protein interactions as drug targets.

Corbi-Verge C, Kim PM.

Cell Commun Signal. 2016 Mar 2;14:8. doi: 10.1186/s12964-016-0131-4. Review.

25.

Pooled screening for antiproliferative inhibitors of protein-protein interactions.

Nim S, Jeon J, Corbi-Verge C, Seo MH, Ivarsson Y, Moffat J, Tarasova N, Kim PM.

Nat Chem Biol. 2016 Apr;12(4):275-81. doi: 10.1038/nchembio.2026. Epub 2016 Feb 22.

26.

A high-throughput pipeline for the production of synthetic antibodies for analysis of ribonucleoprotein complexes.

Na H, Laver JD, Jeon J, Singh F, Ancevicius K, Fan Y, Cao WX, Nie K, Yang Z, Luo H, Wang M, Rissland O, Westwood JT, Kim PM, Smibert CA, Lipshitz HD, Sidhu SS.

RNA. 2016 Apr;22(4):636-55. doi: 10.1261/rna.055186.115. Epub 2016 Feb 4.

27.

ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity.

Witvliet DK, Strokach A, Giraldo-Forero AF, Teyra J, Colak R, Kim PM.

Bioinformatics. 2016 May 15;32(10):1589-91. doi: 10.1093/bioinformatics/btw031. Epub 2016 Jan 21.

PMID:
26801957
28.

Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin.

Garrido-Urbani S, Garg P, Ghossoub R, Arnold R, Lembo F, Sundell GN, Kim PM, Lopez M, Zimmermann P, Sidhu SS, Ivarsson Y.

FEBS Lett. 2016 Jan;590(1):3-12. doi: 10.1002/1873-3468.12037. Epub 2016 Jan 8.

29.

JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis.

Colak R, Kim T, Kazan H, Oh Y, Cruz M, Valladares-Salgado A, Peralta J, Escobedo J, Parra EJ, Kim PM, Goldenberg A.

Bioinformatics. 2016 Jan 15;32(2):203-10. doi: 10.1093/bioinformatics/btv504. Epub 2015 Sep 26.

30.

A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity.

Garton M, Najafabadi HS, Schmitges FW, Radovani E, Hughes TR, Kim PM.

Nucleic Acids Res. 2015 Oct 30;43(19):9147-57. doi: 10.1093/nar/gkv919. Epub 2015 Sep 17.

31.

Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins.

Hao Y, Colak R, Teyra J, Corbi-Verge C, Ignatchenko A, Hahne H, Wilhelm M, Kuster B, Braun P, Kaida D, Kislinger T, Kim PM.

Cell Rep. 2015 Jul 14;12(2):183-9. doi: 10.1016/j.celrep.2015.06.031. Epub 2015 Jul 2.

32.

Photoelectrochemical Cells Utilizing Tunable Corroles.

Brennan BJ, Lam YC, Kim PM, Zhang X, Brudvig GW.

ACS Appl Mater Interfaces. 2015 Jul 29;7(29):16124-30. doi: 10.1021/acsami.5b05050. Epub 2015 Jul 14.

PMID:
26135477
33.

C2H2 zinc finger proteins greatly expand the human regulatory lexicon.

Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR.

Nat Biotechnol. 2015 May;33(5):555-62. doi: 10.1038/nbt.3128. Epub 2015 Feb 18.

PMID:
25690854
34.

The Relationship between Type D Personality and Suicidality in Low-Income, Middle-Aged Adults.

Yoon DH, Kim SJ, Lee JH, Kim PM, Park DH, Ryu SH, Yu J, Ha JH.

Psychiatry Investig. 2015 Jan;12(1):16-22. doi: 10.4306/pi.2015.12.1.16. Epub 2015 Jan 12.

35.

Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation.

Berliner N, Teyra J, Colak R, Garcia Lopez S, Kim PM.

PLoS One. 2014 Sep 22;9(9):e107353. doi: 10.1371/journal.pone.0107353. eCollection 2014.

36.

A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening.

Jeon J, Nim S, Teyra J, Datti A, Wrana JL, Sidhu SS, Moffat J, Kim PM.

Genome Med. 2014 Jul 30;6(7):57. doi: 10.1186/s13073-014-0057-7. eCollection 2014.

37.

Classification of intrinsically disordered regions and proteins.

van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, Kim PM, Kriwacki RW, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright PE, Babu MM.

Chem Rev. 2014 Jul 9;114(13):6589-631. doi: 10.1021/cr400525m. Epub 2014 Apr 29. Review. No abstract available.

38.

Characterizing WW domain interactions of tumor suppressor WWOX reveals its association with multiprotein networks.

Abu-Odeh M, Bar-Mag T, Huang H, Kim T, Salah Z, Abdeen SK, Sudol M, Reichmann D, Sidhu S, Kim PM, Aqeilan RI.

J Biol Chem. 2014 Mar 28;289(13):8865-80. doi: 10.1074/jbc.M113.506790. Epub 2014 Feb 18.

39.

Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes.

Ivarsson Y, Arnold R, McLaughlin M, Nim S, Joshi R, Ray D, Liu B, Teyra J, Pawson T, Moffat J, Li SS, Sidhu SS, Kim PM.

Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2542-7. doi: 10.1073/pnas.1312296111. Epub 2014 Feb 3.

40.

Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity.

Chen C, Ha BH, Thévenin AF, Lou HJ, Zhang R, Yip KY, Peterson JR, Gerstein M, Kim PM, Filippakopoulos P, Knapp S, Boggon TJ, Turk BE.

Mol Cell. 2014 Jan 9;53(1):140-7. doi: 10.1016/j.molcel.2013.11.013. Epub 2013 Dec 26.

41.

A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities.

Vizeacoumar FJ, Arnold R, Vizeacoumar FS, Chandrashekhar M, Buzina A, Young JT, Kwan JH, Sayad A, Mero P, Lawo S, Tanaka H, Brown KR, Baryshnikova A, Mak AB, Fedyshyn Y, Wang Y, Brito GC, Kasimer D, Makhnevych T, Ketela T, Datti A, Babu M, Emili A, Pelletier L, Wrana J, Wainberg Z, Kim PM, Rottapel R, O'Brien CA, Andrews B, Boone C, Moffat J.

Mol Syst Biol. 2013 Oct 8;9:696. doi: 10.1038/msb.2013.54.

42.

Distinct types of disorder in the human proteome: functional implications for alternative splicing.

Colak R, Kim T, Michaut M, Sun M, Irimia M, Bellay J, Myers CL, Blencowe BJ, Kim PM.

PLoS Comput Biol. 2013 Apr;9(4):e1003030. doi: 10.1371/journal.pcbi.1003030. Epub 2013 Apr 25.

43.

Interpreting protein networks with three-dimensional structures.

Teyra J, Kim PM.

Nat Methods. 2013 Jan;10(1):43-4. doi: 10.1038/nmeth.2300. No abstract available.

PMID:
23269376
44.

The evolutionary landscape of alternative splicing in vertebrate species.

Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ.

Science. 2012 Dec 21;338(6114):1587-93. doi: 10.1126/science.1230612.

PMID:
23258890
45.

Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space.

Arnold R, Boonen K, Sun MG, Kim PM.

Methods. 2012 Aug;57(4):508-18. doi: 10.1016/j.ymeth.2012.06.011. Epub 2012 Jun 28. Review.

PMID:
22750305
46.

Tissue-specific alternative splicing remodels protein-protein interaction networks.

Ellis JD, Barrios-Rodiles M, Colak R, Irimia M, Kim T, Calarco JA, Wang X, Pan Q, O'Hanlon D, Kim PM, Wrana JL, Blencowe BJ.

Mol Cell. 2012 Jun 29;46(6):884-92. doi: 10.1016/j.molcel.2012.05.037.

47.

Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains.

Teyra J, Sidhu SS, Kim PM.

FEBS Lett. 2012 Aug 14;586(17):2631-7. doi: 10.1016/j.febslet.2012.05.043. Epub 2012 Jun 9. Review.

48.

Computational structural analysis of protein interactions and networks.

Hooda Y, Kim PM.

Proteomics. 2012 May;12(10):1697-705. doi: 10.1002/pmic.201100597. Review.

PMID:
22593000
49.

Network evolution: rewiring and signatures of conservation in signaling.

Sun MG, Sikora M, Costanzo M, Boone C, Kim PM.

PLoS Comput Biol. 2012;8(3):e1002411. doi: 10.1371/journal.pcbi.1002411. Epub 2012 Mar 15.

50.

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets.

Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM.

Nucleic Acids Res. 2012 Mar;40(6):e47. doi: 10.1093/nar/gkr1294. Epub 2011 Dec 30.

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