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The Faculty of Medicine - Microbiology and Molecular Genetics: Furman Ora


 Last updated June 2021 - School of Pharmacy

List of Publications

(1) Sadeh M, Rahat D, Meiner V, Fellig Y, Arad M, Schueler-Furman O, et al. Multi-system neurological disorder associated with a CRYAB variant. Neurogenetics 2021;22(2):117-125.

(2) Kumar S, Kolodkin-Gal I, Vesper O, Alam N, Schueler-Furman O, Moll I, et al. Correction for kumar et al., “Escherichia coli quorum-sensing EDF, a peptide generated by novel multiple distinct mechanisms and regulated by trans-translation”. mBio 2021;12(1):1.

(3) Mayer G, Shpilt Z, Bressler S, Marcu O, Schueler-Furman O, Tshuva EY, et al. Targeting an Interaction Between Two Disordered Domains by Using a Designed Peptide. Chem Eur J 2020;26(45):10156.

(4) Khramushin A, Marcu O, Alam N, Shimony O, Padhorny D, Brini E, et al. Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45. Proteins Struct Funct Bioinformatics 2020;88(8):1037-1049.

(5) Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, Kotelnikov S, et al. ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking. Proteins Struct Funct Bioinformatics 2020;88(8):1082-1090.

(6) Lahav N, Rotem-Bamberger S, Fahoum J, Dodson E-, Kraus Y, Mousa R, et al. Phosphorylation of the WWOX Protein Regulates Its Interaction with p73. ChemBioChem 2020;21(13):1843-1851.

(7) Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods 2020;17(7):665-680.

(8) Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput Biol 2020;16(5).

(9) Badaczewska-Dawid AE, Khramushin A, Kolinski A, Schueler-Furman O, Kmiecik S. Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures. Methods Mol Biol 2020;2165:273-287.

(10) Mayer G, Shpilt Z, Bressler S, Marcu O, Schueler-Furman O, Tshuva EY, et al. Targeting an Interaction Between Two Disordered Domains by Using a Designed Peptide. Chem Eur J 2020.

(11) Namburi P, Khateb S, Meyer S, Bentovim T, Ratnapriya R, Khramushin A, et al. A unique PRDM13-associated variant in a Georgian Jewish family with probable North Carolina macular dystrophy and the possible contribution of a unique CFH variant. Mol Vision 2020;26:299-310.

(12) Arkadir D, Lossos A, Rahat D, Abu Snineh M, Schueler-Furman O, Nitschke S, et al. MYORG is associated with recessive primary familial brain calcification. Ann Clin Transl Neurol 2019;6(1):106-113.

(13) Karbian N, Eshed-Eisenbach Y, Tabib A, Hoizman H, Paul Morgan B, Schueler-Furman O, et al. Molecular pathogenesis of human CD59 deficiency. Neurol Genet 2018;4(6).

(14) Ben-Menachem R, Wang K, Marcu O, Yu Z, Lim TK, Lin Q, et al. Yeast aconitase mitochondrial import is modulated by interactions of its C and N terminal domains and Ssa1/2 (Hsp70). Sci Rep 2018;8(1).

(15) Ciemny M, Kurcinski M, Kamel K, Kolinski A, Alam N, Schueler-Furman O, et al. Protein–peptide docking: opportunities and challenges. Drug Discov Today 2018;23(8):1530-1537.

(16) Hánová I, Brynda J, Houštecká R, Alam N, Sojka D, Kopáček P, et al. Novel Structural Mechanism of Allosteric Regulation of Aspartic Peptidases via an Evolutionarily Conserved Exosite. Cell Chem Biol 2018;25(3):318-329.e4.

(17) Alam N, Goldstein O, Xia B, Porter KA, Kozakov D, Schueler-Furman O. High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. PLoS Comput Biol 2017;13(12).

(18) Porter KA, Xia B, Beglov D, Bohnuud T, Alam N, Schueler-Furman O, et al. ClusPro PeptiDock: Efficient global docking of peptide recognition motifs using FFT. Bioinformatics 2017;33(20):3299-3301.

(19) Price C, Merchant M, Jones S, Best A, Von Dwingelo J, Lawrenz MB, et al. Host FIH-mediated asparaginyl hydroxylation of translocated Legionella pneumophila effectors. Front Cell Infect Microbiol 2017;7(MAR).

(20) Marcu O, Dodson E-, Alam N, Sperber M, Kozakov D, Lensink MF, et al. FlexPepDock lessons from CAPRI peptide–protein rounds and suggested new criteria for assessment of model quality and utility. Proteins Struct Funct Bioinformatics 2017;85(3):445-462.

(21) Alam N, Schueler-Furman O. Modeling peptide-protein structure and binding using monte carlo sampling approaches: Rosetta flexpepdock and flexpepbind. Methods Mol Biol 2017;1561:139-169.

(22) Bohnuud T, Jones G, Schueler-Furman O, Kozakov D. Detection of peptide-binding sites on protein surfaces using the peptimap server. Methods Mol Biol 2017;1561:11-20.

(23) Bohnuud T, Luo L, Wodak SJ, Bonvin AMJJ, Weng Z, Vajda S, et al. A benchmark testing ground for integrating homology modeling and protein docking. Proteins Struct Funct Bioinformatics 2017;85(1):10-16.

(24) Schueler-Furman O, Wodak SJ. Computational approaches to investigating allostery. Curr Opin Struct Biol 2016;41:159-171.

(25) Sedan Y, Marcu O, Lyskov S, Schueler-Furman O. Peptiderive server: derive peptide inhibitors from protein-protein interactions. Nucleic Acids Res 2016;44(W1):W536-W541.

(26) Levin L, Srour S, Gartner J, Kapitansky O, Qutob N, Dror S, et al. Parkin Somatic Mutations Link Melanoma and Parkinson's Disease. J Genet Genomics 2016;43(6):369-379.

(27) Alam N, Zimmerman L, Wolfson NA, Joseph CG, Fierke CA, Schueler-Furman O. Structure-Based Identification of HDAC8 Non-histone Substrates. Structure 2016;24(3):458-468.

(28) Kumar S, Kolodkin-Gal I, Vesper O, Alam N, Schueler-Furman O, Moll I, et al. Escherichia coli quorum-sensing EDF, a peptide generated by novel multiple distinct mechanisms and regulated by trans-translation. mBio 2016;7(1).

(29) Spiegel R, Saada A, Flannery PJ, Burté F, Soiferman D, Khayat M, et al. Fatal infantile mitochondrial encephalomyopathy, hypertrophic cardiomyopathy and optic atrophy associated with a homozygous OPA1 mutation. J Med Genet 2016;53(2):127-131.

(30) Abu-Remaileh M, Joy-Dodson E, Schueler-Furman O, Aqeilan RI. Pleiotropic functions of tumor suppressor WWOX in normal and cancer cells. J Biol Chem 2015;290(52):30728-30735.

(31) Slutzki M, Reshef D, Barak Y, Haimovitz R, Rotem-Bamberger S, Lamed R, et al. Crucial roles of single residues in binding affinity, specificity, and promiscuity in the cellulosomal cohesin-dockerin interface. J Biol Chem 2015;290(22):13654-13666.

(32) Dodson EJ, Fishbain-Yoskovitz V, Rotem-Bamberger S, Schueler-Furman O. Versatile communication strategies among tandem WW domain repeats. Exp Biol Med 2015;240(3):351-360.

(33) Abdulhag UN, Soiferman D, Schueler-Furman O, Miller C, Shaag A, Elpeleg O, et al. Mitochondrial complex IV deficiency, caused by mutated COX6B1, is associated with encephalomyopathy, hydrocephalus and cardiomyopathy. Eur J Hum Genet 2015;23(2):159-164.

(34) Lossos A, Elazar N, Lerer I, Schueler-Furman O, Fellig Y, Glick B, et al. Myelin-associated glycoprotein gene mutation causes Pelizaeus-Merzbacher disease-like disorder. Brain 2015;138(9):2521-2536.

(35) Gao M, London N, Cheng K, Tamura R, Jin J, Schueler-Furman O, et al. Rationally designed macrocyclic peptides as synergistic agonists of LPS-induced inflammatory response. Tetrahedron 2014;70(42):7664-7668.

(36) Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, et al. Encounter complexes and dimensionality reduction in protein-protein association. eLife 2014;2014(3).

(37) London N, Raveh B, Schueler-Furman O. Druggable protein-protein interactions - from hot spots to hot segments. Curr Opin Chem Biol 2013;17(6):952-959.

(38) London N, Raveh B, Schueler-Furman O. Peptide docking and structure-based characterization of peptide binding: From knowledge to know-how. Curr Opin Struct Biol 2013;23(6):894-902.

(39) Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, et al. Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27. Proteins Struct Funct Bioinformatics 2013;81(12):2201-2209.

(40) Drayman N, Glick Y, Ben-Nun-Shaul O, Zer H, Zlotnick A, Gerber D, et al. Pathogens use structural mimicry of native host ligands as a mechanism for host receptor engagement. Cell Host and Microbe 2013;14(1):63-73.

(41) Burak E, Yogev O, Sheffer S, Schueler-Furman O, Pines O. Evolving dual targeting of a prokaryotic protein in yeast. Mol Biol Evol 2013;30(7):1563-1573.

(42) Chan A-, Grossman T, Zuckerman V, Campigli Di Giammartino D, Moshel O, Scheffner M, et al. C-Abl phosphorylates E6AP and regulates its E3 ubiquitin ligase activity. Biochemistry 2013;52(18):3119-3129.

(43) Lavi A, Ngan CH, Movshovitz-Attias D, Bohnuud T, Yueh C, Beglov D, et al. Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions. Proteins Struct Funct Bioinformatics 2013;81(12):2096-2105.

(44) Slutzki M, Barak Y, Reshef D, Schueler-Furman O, Lamed R, Bayer EA. Indirect ELISA-based approach for comparative measurement of high-affinity cohesin-dockerin interactions. J Mol Recogn 2012;25(11):616-622.

(45) Brenke R, Hall DR, Chuang G-, Comeau SR, Bohnuud T, Beglov D, et al. Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics 2012;28(20):2608-2614.

(46) Wexselblatt E, Oppenheimer-Shaanan Y, Kaspy I, London N, Schueler-Furman O, Yavin E, et al. Relacin, a Novel Antibacterial Agent Targeting the Stringent Response. PLoS Pathog 2012;8(9).

(47) London N, Gullá S, Keating AE, Schueler-Furman O. In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2. Biochemistry 2012;51(29):5841-5850.

(48) London N, Raveh B, Schueler-Furman O. Modeling peptide-protein interactions. Methods Mol Biol 2012;857:375-398.

(49) Slutzki M, Barak Y, Reshef D, Schueler-Furman O, Lamed R, Bayer EA. Measurements of relative binding of cohesin and dockerin mutants using an advanced ELISA technique for high-affinity interactions. Methods Enzymol 2012;510:417-428.

(50) Al-Quadan T, Price CT, London N, Schueler-Furman O, AbuKwaik Y. Anchoring of bacterial effectors to host membranes through host-mediated lipidation by prenylation: A common paradigm. Trends Microbiol 2011;19(12):573-579.

(51) Fleishman SJ, Whitehead TA, Strauch E-, Corn JE, Qin S, Zhou H-, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol 2011;414(2):289-302.

(52) London N, Lamphear CL, Hougland JL, Fierke CA, Schueler-Furman O. Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity. PLoS Comput Biol 2011;7(10).

(53) London N, Raveh B, Cohen E, Fathi G, Schueler-Furman O. Rosetta FlexPepDock web server - High resolution modeling of peptide-protein interactions. Nucleic Acids Res 2011;39(SUPPL. 2):W249-W253.

(54) Raveh B, London N, Zimmerman L, Schueler-Furman O. Rosetta FlexPepDockab-initio: Simultaneous folding, docking and refinement of peptides onto their receptors. PLoS ONE 2011;6(4).

(55) Belitsky M, Avshalom H, Erental A, Yelin I, Kumar S, London N, et al. The Escherichia coli Extracellular Death Factor EDF Induces the Endoribonucleolytic Activities of the Toxins MazF and ChpBK. Mol Cell 2011;41(6):625-635.

(56) Crawley SW, Gharaei MS, Ye Q, Yang Y, Raveh B, London N, et al. Autophosphorylation activates Dictyostelium myosin II heavy chain kinase A by providing a ligand for an allosteric binding site in the α-kinase domain. J Biol Chem 2011;286(4):2607-2616.

(57) London N, Raveh B, Movshovitz-Attias D, Schueler-Furman O. Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions? Proteins Struct Funct Bioinformatics 2010;78(15):3140-3149.

(58) Reshef D, Itzhaki Z, Schueler-Furman O. Increased sequence conservation of domain repeats in prokaryotic proteins. Trends Genet 2010;26(9):383-387.

(59) Movshovitz-Attias D, London N, Schueler-Furman O. On the use of structural templates for high-resolution docking. Proteins Struct Funct Bioinformatics 2010;78(8):1939-1949.

(60) London N, Movshovitz-Attias D, Schueler-Furman O. The Structural Basis of Peptide-Protein Binding Strategies. Structure 2010;18(2):188-199.

(61) London N, Schueler-Furman O. High-resolution protein–protein docking. Protein-Protein Complexes: Analysis, Modeling and Drug Design; 2010. p. 209-235.

(62) Raveh B, London N, Schueler-Furman O. Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins Struct Funct Bioinformatics 2010;78(9):2029-2040.

(63) Kanarek N, London N, Schueler-Furman O, Ben-Neriah Y. Ubiquitination and degradation of the inhibitors of NF-kappaB. Cold Spring Harb Perspect Biol 2010;2(2).

(64) Dassa B, London N, Stoddard BL, Schueler-Furman O, Pietrokovski S. Fractured genes: A novel genomic arrangement involving new split inteins and a new homing endonuclease family. Nucleic Acids Res 2009;37(8):2560-2573.

(65) Ben-nun-Shaul O, Bronfeld H, Reshef D, Schueler-Furman O, Oppenheim A. The SV40 Capsid Is Stabilized by a Conserved Pentapeptide Hinge of the Major Capsid Protein VP1. J Mol Biol 2009;386(5):1382-1391.

(66) Raveh B, Enosh A, Schueler-Furman O, Halperin D. Rapid sampling of molecular motions with prior information constraints. PLoS Comput Biol 2009;5(2).

(67) London N, Schueler-Furman O. FunHunt: Model selection based on energy landscape characteristics. Biochem Soc Trans 2008;36(6):1418-1421.

(68) Enosh A, Raveh B, Furman-Schueler O, Halperin D, Ben-Tal N. Generation, comparison, and merging of pathways between protein conformations: Gating in K-channels. Biophys J 2008;95(8):3850-3860.

(69) Yanover C, Schueler-Furman O, Weiss Y. Minimizing and learning energy functions for side-chain prediction. J Comput Biol 2008;15(7):899-911.

(70) Kozakov D, Schueler-Furman O, Vajda S. Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins Struct Funct Genet 2008;72(3):993-1004.

(71) London N, Schueler-Furman O. Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels. Structure 2008;16(2):269-279.

(72) London N, Schueler-Furman O. Assessing the energy landscape of CAPRI targets by FunHunt. Proteins Struct Funct Genet 2007;69(4):809-815.

(73) Wang C, Schueler-Furman O, Andre I, London N, Fleishman SJ, Bradley P, et al. RosettaDock in CAPRI rounds 6-12. Proteins Struct Funct Genet 2007;69(4):758-763.

(74) Goobes G, Goobes R, Shaw WJ, Gibson JM, Long JR, Raghunathan V, et al. The structure, dynamics, and energetics of protein adsorption - Lessons learned from adsorption of statherin to hydroxyapatite. Magn Reson Chem 2007;45(SUPPL.):S32-S47.

(75) Dassa B, Amitai G, Caspi J, Schueler-Furman O, Pietrokovski S. Trans protein splicing of cyanobacterial split inteins in endogenous and exogenous combinations. Biochemistry 2007;46(1):322-330.

(76) Minimizing and learning energy functions for side-chain prediction. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 2007.

(77) Goobes G, Goobes R, Schueler-Furman O, Baker D, Stayton PS, Drobny GP. Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proc Natl Acad Sci U S A 2006;103(44):16083-16088.

(78) Jojic N, Reyes-Gomez M, Heckerman D, Kadie C, Schueler-Furman O. Learning MHC I - Peptide binding. Bioinformatics 2006;22(14):e227-e235.

(79) Levy C, Lee Y-, Nechushtan H, Schueler-Furman O, Sonnenblick A, Hacohen S, et al. Identifying a common molecular mechanism for inhibition of MITF and STAT3 by PIAS3. Blood 2006;107(7):2839-2845.

(80) Schueler-Furman O, Glick E, Segovia J, Linial M. Is GAS1 a co-receptor for the GDNF family of ligands? Trends Pharmacol Sci 2006;27(2):72-77.

(81) Lacy DB, Lin HC, Melnyk RA, Schueler-Furman O, Reither L, Cunningham K, et al. A model of anthrax toxin lethal factor bound to protective antigen. Proc Natl Acad Sci U S A 2005;102(45):16409-16414.

(82) Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science 2005;310(5748):638-642.

(83) Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins Struct Funct Genet 2005;60(2):187-194.

(84) Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci 2005;14(5):1328-1339.

(85) Bradley P, Chivian D, Meiler J, Misura KMS, Rohl CA, Schief WR, et al. Rosetta Predictions in CASP5: Successes, Failures, and Prospects for Complete Automation. Proteins Struct Funct Genet 2003;53(SUPPL. 6):457-468.

(86) Schueler-Furman O, Baker D. Conserved residue clustering and protein structure prediction. Proteins Struct Funct Genet 2003;52(2):225-235.

(87) Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331(1):281-299.

(88) Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura K, Morozov AV, et al. Protein-protein docking predictions for the CAPRI experiment. Proteins Struct Funct Genet 2003;52(1):118-122.

(89) Schueler-Furman O, Altuvia Y, Margalit H. Differential effects of isomeric incorporation of fluorophenylalanines into PvuII endonuclease. Proteins Struct Funct Genet 2001;45(1):55-61.

(90) Schueler-Furman O, Altuvia Y, Margalit H. Examination of possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins. Proteins Struct Funct Genet 2001;45(1):47-54.

(91) Schueler-Furman O, Altuvia Y, Margalit H. Comparative modeling of CASP4 target proteins: Combining results of sequence search with three-dimensional structure assessment. Proteins Struct Funct Genet 2001;45:47-54.

(92) Schueler-Furman O, Altuvia Y, Sette A, Margalit H. Structure-based prediction of binding peptides to MHC class I molecules: Application to a broad range of MHC alleles. Protein Sci 2000;9(9):1838-1846.

(93) Schueler-Furman O, Elber R, Margalit H. Knowledge-based structure prediction of MHC class I bound peptides: A study of 23 complexes. Fold Design 1998;3(6):549-564.

(94) Mandel-Gutfreund Y, Schueler O, Margalit H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles. J Mol Biol 1995;253(2):370-382.

(95) Schueler O, Margalit H. Conservation of salt bridges in protein families. J Mol Biol 1995;248(1):125-135.

(96) Altuvia Y, Schueler O, Margalit H. Ranking potential binding peptides to MHC molecules by a computational threading approach. J Mol Biol 1995;249(2):244-250.