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Items: 1 to 50 of 74

1.

Protein-peptide docking: opportunities and challenges.

Ciemny M, Kurcinski M, Kamel K, Kolinski A, Alam N, Schueler-Furman O, Kmiecik S.

Drug Discov Today. 2018 Aug;23(8):1530-1537. doi: 10.1016/j.drudis.2018.05.006. Epub 2018 May 4. Review.

2.

Yeast aconitase mitochondrial import is modulated by interactions of its C and N terminal domains and Ssa1/2 (Hsp70).

Ben-Menachem R, Wang K, Marcu O, Yu Z, Lim TK, Lin Q, Schueler-Furman O, Pines O.

Sci Rep. 2018 Apr 12;8(1):5903. doi: 10.1038/s41598-018-24068-w.

3.

Novel Structural Mechanism of Allosteric Regulation of Aspartic Peptidases via an Evolutionarily Conserved Exosite.

Hánová I, Brynda J, Houštecká R, Alam N, Sojka D, Kopáček P, Marešová L, Vondrášek J, Horn M, Schueler-Furman O, Mareš M.

Cell Chem Biol. 2018 Mar 15;25(3):318-329.e4. doi: 10.1016/j.chembiol.2018.01.001. Epub 2018 Jan 27.

PMID:
29396291
4.

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock.

Alam N, Goldstein O, Xia B, Porter KA, Kozakov D, Schueler-Furman O.

PLoS Comput Biol. 2017 Dec 27;13(12):e1005905. doi: 10.1371/journal.pcbi.1005905. eCollection 2017 Dec.

5.

ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT.

Porter KA, Xia B, Beglov D, Bohnuud T, Alam N, Schueler-Furman O, Kozakov D.

Bioinformatics. 2017 Oct 15;33(20):3299-3301. doi: 10.1093/bioinformatics/btx216.

6.

Host FIH-Mediated Asparaginyl Hydroxylation of Translocated Legionella pneumophila Effectors.

Price C, Merchant M, Jones S, Best A, Von Dwingelo J, Lawrenz MB, Alam N, Schueler-Furman O, Kwaik YA.

Front Cell Infect Microbiol. 2017 Mar 6;7:54. doi: 10.3389/fcimb.2017.00054. eCollection 2017.

7.

Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind.

Alam N, Schueler-Furman O.

Methods Mol Biol. 2017;1561:139-169. doi: 10.1007/978-1-4939-6798-8_9.

PMID:
28236237
8.

Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server.

Bohnuud T, Jones G, Schueler-Furman O, Kozakov D.

Methods Mol Biol. 2017;1561:11-20. doi: 10.1007/978-1-4939-6798-8_2.

PMID:
28236230
9.

FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility.

Marcu O, Dodson EJ, Alam N, Sperber M, Kozakov D, Lensink MF, Schueler-Furman O.

Proteins. 2017 Mar;85(3):445-462. doi: 10.1002/prot.25230.

PMID:
28002624
10.

Computational approaches to investigating allostery.

Schueler-Furman O, Wodak SJ.

Curr Opin Struct Biol. 2016 Dec;41:159-171. doi: 10.1016/j.sbi.2016.06.017. Epub 2016 Sep 6. Review.

PMID:
27607077
11.

Parkin Somatic Mutations Link Melanoma and Parkinson's Disease.

Levin L, Srour S, Gartner J, Kapitansky O, Qutob N, Dror S, Golan T, Dayan R, Brener R, Ziv T, Khaled M, Schueler-Furman O, Samuels Y, Levy C.

J Genet Genomics. 2016 Jun 20;43(6):369-79. doi: 10.1016/j.jgg.2016.05.005. Epub 2016 May 13.

PMID:
27297116
12.

A benchmark testing ground for integrating homology modeling and protein docking.

Bohnuud T, Luo L, Wodak SJ, Bonvin AM, Weng Z, Vajda S, Schueler-Furman O, Kozakov D.

Proteins. 2017 Jan;85(1):10-16. doi: 10.1002/prot.25063. Epub 2016 Nov 13.

13.

Peptiderive server: derive peptide inhibitors from protein-protein interactions.

Sedan Y, Marcu O, Lyskov S, Schueler-Furman O.

Nucleic Acids Res. 2016 Jul 8;44(W1):W536-41. doi: 10.1093/nar/gkw385. Epub 2016 May 3.

14.

Structure-Based Identification of HDAC8 Non-histone Substrates.

Alam N, Zimmerman L, Wolfson NA, Joseph CG, Fierke CA, Schueler-Furman O.

Structure. 2016 Mar 1;24(3):458-68. doi: 10.1016/j.str.2016.02.002.

15.

Escherichia coli Quorum-Sensing EDF, A Peptide Generated by Novel Multiple Distinct Mechanisms and Regulated by trans-Translation.

Kumar S, Kolodkin-Gal I, Vesper O, Alam N, Schueler-Furman O, Moll I, Engelberg-Kulka H.

MBio. 2016 Jan 26;7(1):e02034-15. doi: 10.1128/mBio.02034-15.

16.

Pleiotropic Functions of Tumor Suppressor WWOX in Normal and Cancer Cells.

Abu-Remaileh M, Joy-Dodson E, Schueler-Furman O, Aqeilan RI.

J Biol Chem. 2015 Dec 25;290(52):30728-35. doi: 10.1074/jbc.R115.676346. Epub 2015 Oct 23. Review.

17.

Myelin-associated glycoprotein gene mutation causes Pelizaeus-Merzbacher disease-like disorder.

Lossos A, Elazar N, Lerer I, Schueler-Furman O, Fellig Y, Glick B, Zimmerman BE, Azulay H, Dotan S, Goldberg S, Gomori JM, Ponger P, Newman JP, Marreed H, Steck AJ, Schaeren-Wiemers N, Mor N, Harel M, Geiger T, Eshed-Eisenbach Y, Meiner V, Peles E.

Brain. 2015 Sep;138(Pt 9):2521-36. doi: 10.1093/brain/awv204. Epub 2015 Jul 15.

18.

Crucial roles of single residues in binding affinity, specificity, and promiscuity in the cellulosomal cohesin-dockerin interface.

Slutzki M, Reshef D, Barak Y, Haimovitz R, Rotem-Bamberger S, Lamed R, Bayer EA, Schueler-Furman O.

J Biol Chem. 2015 May 29;290(22):13654-66. doi: 10.1074/jbc.M115.651208. Epub 2015 Apr 1.

19.

Versatile communication strategies among tandem WW domain repeats.

Dodson EJ, Fishbain-Yoskovitz V, Rotem-Bamberger S, Schueler-Furman O.

Exp Biol Med (Maywood). 2015 Mar;240(3):351-60. doi: 10.1177/1535370214566558. Epub 2015 Feb 20. Review.

20.

Rationally Designed Macrocyclic Peptides as Synergistic Agonists of LPS-Induced Inflammatory Response.

Gao M, London N, Cheng K, Tamura R, Jin J, Schueler-Furman O, Yin H.

Tetrahedron. 2014 Oct 21;70(42):7664-7668. doi: 10.1016/j.tet.2014.07.026.

21.

Mitochondrial complex IV deficiency, caused by mutated COX6B1, is associated with encephalomyopathy, hydrocephalus and cardiomyopathy.

Abdulhag UN, Soiferman D, Schueler-Furman O, Miller C, Shaag A, Elpeleg O, Edvardson S, Saada A.

Eur J Hum Genet. 2015 Feb;23(2):159-64. doi: 10.1038/ejhg.2014.85. Epub 2014 Apr 30.

22.

Encounter complexes and dimensionality reduction in protein-protein association.

Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, Schueler-Furman O, Paschalidis ICh, Clore GM, Vajda S.

Elife. 2014 Apr 8;3:e01370. doi: 10.7554/eLife.01370.

23.

Druggable protein-protein interactions--from hot spots to hot segments.

London N, Raveh B, Schueler-Furman O.

Curr Opin Chem Biol. 2013 Dec;17(6):952-9. doi: 10.1016/j.cbpa.2013.10.011. Epub 2013 Oct 31. Review.

PMID:
24183815
24.

Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how.

London N, Raveh B, Schueler-Furman O.

Curr Opin Struct Biol. 2013 Dec;23(6):894-902. doi: 10.1016/j.sbi.2013.07.006. Epub 2013 Oct 15. Review.

PMID:
24138780
25.

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27.

Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ.

Proteins. 2013 Dec;81(12):2201-9. doi: 10.1002/prot.24425. Epub 2013 Oct 17.

26.

Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions.

Lavi A, Ngan CH, Movshovitz-Attias D, Bohnuud T, Yueh C, Beglov D, Schueler-Furman O, Kozakov D.

Proteins. 2013 Dec;81(12):2096-105. doi: 10.1002/prot.24422. Epub 2013 Oct 17.

27.

Pathogens use structural mimicry of native host ligands as a mechanism for host receptor engagement.

Drayman N, Glick Y, Ben-nun-shaul O, Zer H, Zlotnick A, Gerber D, Schueler-Furman O, Oppenheim A.

Cell Host Microbe. 2013 Jul 17;14(1):63-73. doi: 10.1016/j.chom.2013.05.005.

28.

c-Abl phosphorylates E6AP and regulates its E3 ubiquitin ligase activity.

Chan AL, Grossman T, Zuckerman V, Campigli Di Giammartino D, Moshel O, Scheffner M, Monahan B, Pilling P, Jiang YH, Haupt S, Schueler-Furman O, Haupt Y.

Biochemistry. 2013 May 7;52(18):3119-29. doi: 10.1021/bi301710c. Epub 2013 Apr 26.

PMID:
23581475
29.

Evolving dual targeting of a prokaryotic protein in yeast.

Burak E, Yogev O, Sheffer S, Schueler-Furman O, Pines O.

Mol Biol Evol. 2013 Jul;30(7):1563-73. doi: 10.1093/molbev/mst039. Epub 2013 Mar 5.

PMID:
23462316
30.

Indirect ELISA-based approach for comparative measurement of high-affinity cohesin-dockerin interactions.

Slutzki M, Barak Y, Reshef D, Schueler-Furman O, Lamed R, Bayer EA.

J Mol Recognit. 2012 Nov;25(11):616-22. doi: 10.1002/jmr.2178.

PMID:
23108621
31.

Application of asymmetric statistical potentials to antibody-protein docking.

Brenke R, Hall DR, Chuang GY, Comeau SR, Bohnuud T, Beglov D, Schueler-Furman O, Vajda S, Kozakov D.

Bioinformatics. 2012 Oct 15;28(20):2608-14. doi: 10.1093/bioinformatics/bts493.

32.

Relacin, a novel antibacterial agent targeting the Stringent Response.

Wexselblatt E, Oppenheimer-Shaanan Y, Kaspy I, London N, Schueler-Furman O, Yavin E, Glaser G, Katzhendler J, Ben-Yehuda S.

PLoS Pathog. 2012 Sep;8(9):e1002925. doi: 10.1371/journal.ppat.1002925. Epub 2012 Sep 20.

33.

In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2.

London N, Gullá S, Keating AE, Schueler-Furman O.

Biochemistry. 2012 Jul 24;51(29):5841-50. doi: 10.1021/bi3003567. Epub 2012 Jul 12.

34.

Measurements of relative binding of cohesin and dockerin mutants using an advanced ELISA technique for high-affinity interactions.

Slutzki M, Barak Y, Reshef D, Schueler-Furman O, Lamed R, Bayer EA.

Methods Enzymol. 2012;510:417-28. doi: 10.1016/B978-0-12-415931-0.00022-7.

PMID:
22608739
35.

Modeling peptide-protein interactions.

London N, Raveh B, Schueler-Furman O.

Methods Mol Biol. 2012;857:375-98. doi: 10.1007/978-1-61779-588-6_17.

PMID:
22323231
36.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D.

J Mol Biol. 2011 Nov 25;414(2):289-302. doi: 10.1016/j.jmb.2011.09.031. Epub 2011 Sep 29.

37.

Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity.

London N, Lamphear CL, Hougland JL, Fierke CA, Schueler-Furman O.

PLoS Comput Biol. 2011 Oct;7(10):e1002170. doi: 10.1371/journal.pcbi.1002170. Epub 2011 Oct 6.

38.

Anchoring of bacterial effectors to host membranes through host-mediated lipidation by prenylation: a common paradigm.

Al-Quadan T, Price CT, London N, Schueler-Furman O, AbuKwaik Y.

Trends Microbiol. 2011 Dec;19(12):573-9. doi: 10.1016/j.tim.2011.08.003. Epub 2011 Oct 7.

PMID:
21983544
39.

Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions.

London N, Raveh B, Cohen E, Fathi G, Schueler-Furman O.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W249-53. doi: 10.1093/nar/gkr431. Epub 2011 May 27.

40.

Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors.

Raveh B, London N, Zimmerman L, Schueler-Furman O.

PLoS One. 2011 Apr 29;6(4):e18934. doi: 10.1371/journal.pone.0018934.

41.

The Escherichia coli extracellular death factor EDF induces the endoribonucleolytic activities of the toxins MazF and ChpBK.

Belitsky M, Avshalom H, Erental A, Yelin I, Kumar S, London N, Sperber M, Schueler-Furman O, Engelberg-Kulka H.

Mol Cell. 2011 Mar 18;41(6):625-35. doi: 10.1016/j.molcel.2011.02.023.

42.

Autophosphorylation activates Dictyostelium myosin II heavy chain kinase A by providing a ligand for an allosteric binding site in the alpha-kinase domain.

Crawley SW, Gharaei MS, Ye Q, Yang Y, Raveh B, London N, Schueler-Furman O, Jia Z, Côté GP.

J Biol Chem. 2011 Jan 28;286(4):2607-16. doi: 10.1074/jbc.M110.177014. Epub 2010 Nov 11.

43.

Increased sequence conservation of domain repeats in prokaryotic proteins.

Reshef D, Itzhaki Z, Schueler-Furman O.

Trends Genet. 2010 Sep;26(9):383-7. doi: 10.1016/j.tig.2010.06.003. Epub 2010 Jul 17.

PMID:
20643491
44.

Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions?

London N, Raveh B, Movshovitz-Attias D, Schueler-Furman O.

Proteins. 2010 Nov 15;78(15):3140-9. doi: 10.1002/prot.22785.

45.

Sub-angstrom modeling of complexes between flexible peptides and globular proteins.

Raveh B, London N, Schueler-Furman O.

Proteins. 2010 Jul;78(9):2029-40. doi: 10.1002/prot.22716.

PMID:
20455260
46.

On the use of structural templates for high-resolution docking.

Movshovitz-Attias D, London N, Schueler-Furman O.

Proteins. 2010 Jun;78(8):1939-49. doi: 10.1002/prot.22710.

PMID:
20408170
47.

Ubiquitination and degradation of the inhibitors of NF-kappaB.

Kanarek N, London N, Schueler-Furman O, Ben-Neriah Y.

Cold Spring Harb Perspect Biol. 2010 Feb;2(2):a000166. doi: 10.1101/cshperspect.a000166. Review.

48.

The structural basis of peptide-protein binding strategies.

London N, Movshovitz-Attias D, Schueler-Furman O.

Structure. 2010 Feb 10;18(2):188-99. doi: 10.1016/j.str.2009.11.012.

49.

Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family.

Dassa B, London N, Stoddard BL, Schueler-Furman O, Pietrokovski S.

Nucleic Acids Res. 2009 May;37(8):2560-73. doi: 10.1093/nar/gkp095. Epub 2009 Mar 5.

50.

Rapid sampling of molecular motions with prior information constraints.

Raveh B, Enosh A, Schueler-Furman O, Halperin D.

PLoS Comput Biol. 2009 Feb;5(2):e1000295. doi: 10.1371/journal.pcbi.1000295. Epub 2009 Feb 27.

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