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Items: 1 to 50 of 270

1.

Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior.

Brasch J, Katsamba PS, Harrison OJ, Ahlsén G, Troyanovsky RB, Indra I, Kaczynska A, Kaeser B, Troyanovsky S, Honig B, Shapiro L.

Cell Rep. 2018 May 8;23(6):1840-1852. doi: 10.1016/j.celrep.2018.04.012.

2.

Spatial and temporal organization of cadherin in punctate adherens junctions.

Indra I, Choi J, Chen CS, Troyanovsky RB, Shapiro L, Honig B, Troyanovsky SM.

Proc Natl Acad Sci U S A. 2018 May 8;115(19):E4406-E4415. doi: 10.1073/pnas.1720826115. Epub 2018 Apr 24.

PMID:
29691319
3.

Pathogenic IgG4 autoantibodies from endemic pemphigus foliaceus recognize a desmoglein-1 conformational epitope.

Evangelista F, Roth AJ, Prisayanh P, Temple BR, Li N, Qian Y, Culton DA, Liu Z, Harrison OJ, Brasch J, Honig B, Shapiro L, Diaz LA.

J Autoimmun. 2018 May;89:171-185. doi: 10.1016/j.jaut.2017.12.017. Epub 2018 Jan 4.

PMID:
29307589
4.

Structure-based prediction of ligand-protein interactions on a genome-wide scale.

Hwang H, Dey F, Petrey D, Honig B.

Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):13685-13690. doi: 10.1073/pnas.1705381114. Epub 2017 Dec 11.

5.

Protocadherin cis-dimer architecture and recognition unit diversity.

Goodman KM, Rubinstein R, Dan H, Bahna F, Mannepalli S, Ahlsén G, Aye Thu C, Sampogna RV, Maniatis T, Honig B, Shapiro L.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9829-E9837. doi: 10.1073/pnas.1713449114. Epub 2017 Oct 30.

6.

Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.

Chiu TP, Rao S, Mann RS, Honig B, Rohs R.

Nucleic Acids Res. 2017 Dec 1;45(21):12565-12576. doi: 10.1093/nar/gkx915.

7.

Discovery of an O-mannosylation pathway selectively serving cadherins and protocadherins.

Larsen ISB, Narimatsu Y, Joshi HJ, Siukstaite L, Harrison OJ, Brasch J, Goodman KM, Hansen L, Shapiro L, Honig B, Vakhrushev SY, Clausen H, Halim A.

Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):11163-11168. doi: 10.1073/pnas.1708319114. Epub 2017 Oct 2.

8.

Mutli-features Predction of Protein Translational Modification Sites.

Bao W, Yuan CA, Zhang Y, Han K, Nandi AK, Honig B, Huang DS.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep 28. doi: 10.1109/TCBB.2017.2752703. [Epub ahead of print]

PMID:
28961121
9.

Structural origins of clustered protocadherin-mediated neuronal barcoding.

Rubinstein R, Goodman KM, Maniatis T, Shapiro L, Honig B.

Semin Cell Dev Biol. 2017 Sep;69:140-150. doi: 10.1016/j.semcdb.2017.07.023. Epub 2017 Jul 22. Review.

PMID:
28743640
10.

Mammalian O-mannosylation of cadherins and plexins is independent of protein O-mannosyltransferases 1 and 2.

Larsen ISB, Narimatsu Y, Joshi HJ, Yang Z, Harrison OJ, Brasch J, Shapiro L, Honig B, Vakhrushev SY, Clausen H, Halim A.

J Biol Chem. 2017 Jul 7;292(27):11586-11598. doi: 10.1074/jbc.M117.794487. Epub 2017 May 16.

11.

Genetic Drivers of Kidney Defects in the DiGeorge Syndrome.

Lopez-Rivera E, Liu YP, Verbitsky M, Anderson BR, Capone VP, Otto EA, Yan Z, Mitrotti A, Martino J, Steers NJ, Fasel DA, Vukojevic K, Deng R, Racedo SE, Liu Q, Werth M, Westland R, Vivante A, Makar GS, Bodria M, Sampson MG, Gillies CE, Vega-Warner V, Maiorana M, Petrey DS, Honig B, Lozanovski VJ, Salomon R, Heidet L, Carpentier W, Gaillard D, Carrea A, Gesualdo L, Cusi D, Izzi C, Scolari F, van Wijk JA, Arapovic A, Saraga-Babic M, Saraga M, Kunac N, Samii A, McDonald-McGinn DM, Crowley TB, Zackai EH, Drozdz D, Miklaszewska M, Tkaczyk M, Sikora P, Szczepanska M, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Darlow JM, Puri P, Barton D, Casolari E, Furth SL, Warady BA, Gucev Z, Hakonarson H, Flogelova H, Tasic V, Latos-Bielenska A, Materna-Kiryluk A, Allegri L, Wong CS, Drummond IA, D'Agati V, Imamoto A, Barasch JM, Hildebrandt F, Kiryluk K, Lifton RP, Morrow BE, Jeanpierre C, Papaioannou VE, Ghiggeri GM, Gharavi AG, Katsanis N, Sanna-Cherchi S.

N Engl J Med. 2017 Feb 23;376(8):742-754. doi: 10.1056/NEJMoa1609009. Epub 2017 Jan 25.

12.

A High-Throughput Strategy for Dissecting Mammalian Genetic Interactions.

Stockman VB, Ghamsari L, Lasso G, Honig B, Shapira SD, Wang HH.

PLoS One. 2016 Dec 9;11(12):e0167617. doi: 10.1371/journal.pone.0167617. eCollection 2016.

13.

Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1.

Clark AJ, Gindin T, Zhang B, Wang L, Abel R, Murret CS, Xu F, Bao A, Lu NJ, Zhou T, Kwong PD, Shapiro L, Honig B, Friesner RA.

J Mol Biol. 2017 Apr 7;429(7):930-947. doi: 10.1016/j.jmb.2016.11.021. Epub 2016 Nov 28.

14.

Silencing c-Myc translation as a therapeutic strategy through targeting PI3Kδ and CK1ε in hematological malignancies.

Deng C, Lipstein MR, Scotto L, Jirau Serrano XO, Mangone MA, Li S, Vendome J, Hao Y, Xu X, Deng SX, Realubit RB, Tatonetti NP, Karan C, Lentzsch S, Fruman DA, Honig B, Landry DW, O'Connor OA.

Blood. 2017 Jan 5;129(1):88-99. doi: 10.1182/blood-2016-08-731240. Epub 2016 Oct 26.

15.

γ-Protocadherin structural diversity and functional implications.

Goodman KM, Rubinstein R, Thu CA, Mannepalli S, Bahna F, Ahlsén G, Rittenhouse C, Maniatis T, Honig B, Shapiro L.

Elife. 2016 Oct 26;5. pii: e20930. doi: 10.7554/eLife.20930.

16.

A computational interactome and functional annotation for the human proteome.

Garzón JI, Deng L, Murray D, Shapira S, Petrey D, Honig B.

Elife. 2016 Oct 22;5. pii: e18715. doi: 10.7554/eLife.18715.

17.

Molecular basis of sidekick-mediated cell-cell adhesion and specificity.

Goodman KM, Yamagata M, Jin X, Mannepalli S, Katsamba PS, Ahlsén G, Sergeeva AP, Honig B, Sanes JR, Shapiro L.

Elife. 2016 Sep 19;5. pii: e19058. doi: 10.7554/eLife.19058.

18.

Acetylation-regulated interaction between p53 and SET reveals a widespread regulatory mode.

Wang D, Kon N, Lasso G, Jiang L, Leng W, Zhu WG, Qin J, Honig B, Gu W.

Nature. 2016 Oct 6;538(7623):118-122. doi: 10.1038/nature19759. Epub 2016 Sep 14.

19.

Lipids Regulate Lck Protein Activity through Their Interactions with the Lck Src Homology 2 Domain.

Sheng R, Jung DJ, Silkov A, Kim H, Singaram I, Wang ZG, Xin Y, Kim E, Park MJ, Thiagarajan-Rosenkranz P, Smrt S, Honig B, Baek K, Ryu S, Lorieau J, Kim YM, Cho W.

J Biol Chem. 2016 Aug 19;291(34):17639-50. doi: 10.1074/jbc.M116.720284. Epub 2016 Jun 22.

20.

Structural basis of adhesive binding by desmocollins and desmogleins.

Harrison OJ, Brasch J, Lasso G, Katsamba PS, Ahlsen G, Honig B, Shapiro L.

Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):7160-5. doi: 10.1073/pnas.1606272113. Epub 2016 Jun 13.

21.

Structural Basis of Diverse Homophilic Recognition by Clustered α- and β-Protocadherins.

Goodman KM, Rubinstein R, Thu CA, Bahna F, Mannepalli S, Ahlsén G, Rittenhouse C, Maniatis T, Honig B, Shapiro L.

Neuron. 2016 May 18;90(4):709-23. doi: 10.1016/j.neuron.2016.04.004. Epub 2016 May 5.

22.

Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis.

Westphalen CB, Takemoto Y, Tanaka T, Macchini M, Jiang Z, Renz BW, Chen X, Ormanns S, Nagar K, Tailor Y, May R, Cho Y, Asfaha S, Worthley DL, Hayakawa Y, Urbanska AM, Quante M, Reichert M, Broyde J, Subramaniam PS, Remotti H, Su GH, Rustgi AK, Friedman RA, Honig B, Califano A, Houchen CW, Olive KP, Wang TC.

Cell Stem Cell. 2016 Apr 7;18(4):441-55. doi: 10.1016/j.stem.2016.03.016.

23.

SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins.

Park MJ, Sheng R, Silkov A, Jung DJ, Wang ZG, Xin Y, Kim H, Thiagarajan-Rosenkranz P, Song S, Yoon Y, Nam W, Kim I, Kim E, Lee DG, Chen Y, Singaram I, Wang L, Jang MH, Hwang CS, Honig B, Ryu S, Lorieau J, Kim YM, Cho W.

Mol Cell. 2016 Apr 7;62(1):7-20. doi: 10.1016/j.molcel.2016.01.027. Epub 2016 Mar 24.

24.

Molecular logic of neuronal self-recognition through protocadherin domain interactions.

Rubinstein R, Thu CA, Goodman KM, Wolcott HN, Bahna F, Mannepalli S, Ahlsen G, Chevee M, Halim A, Clausen H, Maniatis T, Shapiro L, Honig B.

Cell. 2015 Oct 22;163(3):629-42. doi: 10.1016/j.cell.2015.09.026. Epub 2015 Oct 17.

25.

p21-activated Kinases (PAKs) Mediate the Phosphorylation of PREX2 Protein to Initiate Feedback Inhibition of Rac1 GTPase.

Barrows D, Schoenfeld SM, Hodakoski C, Silkov A, Honig B, Couvillon A, Shymanets A, Nürnberg B, Asara JM, Parsons R.

J Biol Chem. 2015 Nov 27;290(48):28915-31. doi: 10.1074/jbc.M115.668244. Epub 2015 Oct 5.

26.

E-cadherin junction formation involves an active kinetic nucleation process.

Biswas KH, Hartman KL, Yu CH, Harrison OJ, Song H, Smith AW, Huang WY, Lin WC, Guo Z, Padmanabhan A, Troyanovsky SM, Dustin ML, Shapiro L, Honig B, Zaidel-Bar R, Groves JT.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):10932-7. doi: 10.1073/pnas.1513775112. Epub 2015 Aug 19. Erratum in: Proc Natl Acad Sci U S A. 2016 Nov 14;:. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7870.

27.

α-Catenin-mediated cadherin clustering couples cadherin and actin dynamics.

Chen CS, Hong S, Indra I, Sergeeva AP, Troyanovsky RB, Shapiro L, Honig B, Troyanovsky SM.

J Cell Biol. 2015 Aug 17;210(4):647-61. doi: 10.1083/jcb.201412064. Epub 2015 Aug 10.

28.

A hybrid method for protein-protein interface prediction.

Hwang H, Petrey D, Honig B.

Protein Sci. 2016 Jan;25(1):159-65. doi: 10.1002/pro.2744. Epub 2015 Jul 21.

29.

Predicting peptide-mediated interactions on a genome-wide scale.

Chen TS, Petrey D, Garzon JI, Honig B.

PLoS Comput Biol. 2015 May 4;11(5):e1004248. doi: 10.1371/journal.pcbi.1004248. eCollection 2015 May.

30.

Template-based prediction of protein function.

Petrey D, Chen TS, Deng L, Garzon JI, Hwang H, Lasso G, Lee H, Silkov A, Honig B.

Curr Opin Struct Biol. 2015 Jun;32:33-8. doi: 10.1016/j.sbi.2015.01.007. Epub 2015 Feb 10. Review.

31.

Structural and energetic determinants of adhesive binding specificity in type I cadherins.

Vendome J, Felsovalyi K, Song H, Yang Z, Jin X, Brasch J, Harrison OJ, Ahlsen G, Bahna F, Kaczynska A, Katsamba PS, Edmond D, Hubbell WL, Shapiro L, Honig B.

Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):E4175-84. doi: 10.1073/pnas.1416737111. Epub 2014 Sep 24.

32.

An ankyrin repeat domain of AKR2 drives chloroplast targeting through coincident binding of two chloroplast lipids.

Kim DH, Park MJ, Gwon GH, Silkov A, Xu ZY, Yang EC, Song S, Song K, Kim Y, Yoon HS, Honig B, Cho W, Cho Y, Hwang I.

Dev Cell. 2014 Sep 8;30(5):598-609. doi: 10.1016/j.devcel.2014.07.026.

33.

Single-cell identity generated by combinatorial homophilic interactions between α, β, and γ protocadherins.

Thu CA, Chen WV, Rubinstein R, Chevee M, Wolcott HN, Felsovalyi KO, Tapia JC, Shapiro L, Honig B, Maniatis T.

Cell. 2014 Aug 28;158(5):1045-1059. doi: 10.1016/j.cell.2014.07.012.

34.

Structural bioinformatics of the interactome.

Petrey D, Honig B.

Annu Rev Biophys. 2014;43:193-210. doi: 10.1146/annurev-biophys-051013-022726. Review.

35.

OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites.

Shazman S, Lee H, Socol Y, Mann RS, Honig B.

Nucleic Acids Res. 2014 Jan;42(Database issue):D167-71. doi: 10.1093/nar/gkt1165. Epub 2013 Nov 22.

36.

Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion.

Li Y, Altorelli NL, Bahna F, Honig B, Shapiro L, Palmer AG 3rd.

Proc Natl Acad Sci U S A. 2013 Oct 8;110(41):16462-7. doi: 10.1073/pnas.1314303110. Epub 2013 Sep 25. Erratum in: Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19651.

37.

Theory and simulations of adhesion receptor dimerization on membrane surfaces.

Wu Y, Honig B, Ben-Shaul A.

Biophys J. 2013 Mar 19;104(6):1221-9. doi: 10.1016/j.bpj.2013.02.009. Epub 2013 Mar 19.

38.

Toward a "structural BLAST": using structural relationships to infer function.

Dey F, Cliff Zhang Q, Petrey D, Honig B.

Protein Sci. 2013 Apr;22(4):359-66. doi: 10.1002/pro.2225. Epub 2013 Feb 21. Review.

39.

PrePPI: a structure-informed database of protein-protein interactions.

Zhang QC, Petrey D, Garzón JI, Deng L, Honig B.

Nucleic Acids Res. 2013 Jan;41(Database issue):D828-33. doi: 10.1093/nar/gks1231. Epub 2012 Nov 27.

40.

Structure-based prediction of protein-protein interactions on a genome-wide scale.

Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B.

Nature. 2012 Oct 25;490(7421):556-60. doi: 10.1038/nature11503. Epub 2012 Sep 30. Erratum in: Nature. 2013 Mar 7;495(7439):127.

41.

Nectin ectodomain structures reveal a canonical adhesive interface.

Harrison OJ, Vendome J, Brasch J, Jin X, Hong S, Katsamba PS, Ahlsen G, Troyanovsky RB, Troyanovsky SM, Honig B, Shapiro L.

Nat Struct Mol Biol. 2012 Sep;19(9):906-15. doi: 10.1038/nsmb.2366. Epub 2012 Aug 19.

42.

Thinking outside the cell: how cadherins drive adhesion.

Brasch J, Harrison OJ, Honig B, Shapiro L.

Trends Cell Biol. 2012 Jun;22(6):299-310. doi: 10.1016/j.tcb.2012.03.004. Epub 2012 May 1. Review.

43.

Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions.

Chen Y, Sheng R, Källberg M, Silkov A, Tun MP, Bhardwaj N, Kurilova S, Hall RA, Honig B, Lu H, Cho W.

Mol Cell. 2012 Apr 27;46(2):226-37. doi: 10.1016/j.molcel.2012.02.012. Epub 2012 Mar 22.

44.

Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771.

Eletsky A, Petrey D, Zhang QC, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Honig B, Montelione GT, Szyperski T.

J Struct Funct Genomics. 2012 Mar;13(1):1-7. doi: 10.1007/s10969-011-9121-3. Epub 2012 Jan 6. Erratum in: J Struct Funct Genomics. 2012 Mar;13(1):47.

45.

Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca²+-free interdomain linkers.

Jin X, Walker MA, Felsövályi K, Vendome J, Bahna F, Mannepalli S, Cosmanescu F, Ahlsen G, Honig B, Shapiro L.

Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):E127-34. doi: 10.1073/pnas.1117538108. Epub 2011 Dec 14.

46.

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.

Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS.

Cell. 2011 Dec 9;147(6):1270-82. doi: 10.1016/j.cell.2011.10.053.

47.

Using systems and structure biology tools to dissect cellular phenotypes.

Floratos A, Honig B, Pe'er D, Califano A.

J Am Med Inform Assoc. 2012 Mar-Apr;19(2):171-5. doi: 10.1136/amiajnl-2011-000490. Epub 2011 Nov 10.

48.

Using structure to explore the sequence alignment space of remote homologs.

Kuziemko A, Honig B, Petrey D.

PLoS Comput Biol. 2011 Oct;7(10):e1002175. doi: 10.1371/journal.pcbi.1002175. Epub 2011 Oct 6.

49.

Bridging worlds. Interview by Kristie Nybo.

Honig B.

Biotechniques. 2011 Oct;51(4):225. doi: 10.2144/000113744. No abstract available.

PMID:
21988686
50.

A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.

Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD.

ACS Chem Biol. 2011 Dec 16;6(12):1314-20. doi: 10.1021/cb200155t. Epub 2011 Oct 13.

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