List of Publications


Marcu, Dodson, Alam, Sperber, Kozakov, Lensink & Schueler-Furman (2017).
FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility. Proteins doi: 10.1002/prot.25230.

Bohnuud, Luo, Wodak, Bonvin, Weng, Vajda, Schueler-Furman & Kozakov (2017).
A benchmark testing ground for integrating homology modeling and protein docking. Proteins 85:10-16.


Alam, Zimmerman, Wolfson, Joseph, Fierke & Schueler-Furman (2016).
Structure-Based Identification of HDAC8 Non-histone Substrates. Structure 24:458-468.

Sedan, Marcu, Lyskov & Schueler-Furman (2016).
Peptiderive server: derive peptide inhibitors from protein-protein interactions. Nucleic Acids Res. 44(W1):W536-541.

Schueler-Furman & Wodak (2016).
Computational approaches to investigating allostery. Current Opinion in Structural Biology 41:159-171.

Kumar, Kolodkin-Gal, Vesper, Alam, Schueler-Furman, Moll & Engelberg-Kulka (2016).
Escherichia coli Quorum-Sensing EDF, A Peptide Generated by Novel Multiple Distinct Mechanisms and Regulated by trans-Translation. MBio. 7:e02034-15.

Levin, Srour, Gartner, Kapitansky, Qutob, Dror, Golan, Dayan, Brener, Ziv, Khaled, Schueler-Furman, Samuels & Levy (2016).
Parkin Somatic Mutations Link Melanoma and Parkinson's Disease. Journal of Genetics and Genomics 43:369-370.


Slutzki, Reshef, Barak, Haimovitz, Rotem-Bamberger, Lamed, Bayer & Schueler-Furman (2015).
Crucial roles of single residues in binding affinity, specificity and promiscuity in the cellulosomal cohesin-dockerin interface. J Biol Chem 290:13654-66.

Dodson, Fishbain-Yoskovitz, Rotem-Bamberger, Schueler-Furman (2015).
Versatile communication strategies among tandem WW domain repeats. Exp Biol Med 240:351-60.

Abu-Remaileh, Dodson, Schueler-Furman, Aqeilan (2015).
Pleiotropic Functions of Tumor Suppressor WWOX in Normal and Cancer Cells. J Biol Chem. 290:13654-66.


Gao, London, Cheng, Tamura, Jin, Schueler-Furman, Yin (2014).
Rationally Designed Macrocyclic Peptides as Synergistic Agonists of LPS-Induced Inflammatory Response. Tetrahedron 70:7664-8.

Abdulhag, Soiferman, Schueler-Furman, Miller, Shaag, Elpeleg, Edvardson, Saada (2014).
Mitochondrial complex IV deficiency, caused by mutated COX6B1, is associated with encephalomyopathy, hydrocephalus and cardiomyopathy. Eur J Hum Genet. 23:159-64.

Kozakov, Li, Hall, Beglov, Zheng, Vakili, Schueler-Furman, Paschalidis, Clore, Vajda (2014).
Encounter complexes and dimensionality reduction in protein-protein association. Elife 3:e01370.


London, Raveh, Schueler-Furman (2013).
Druggable protein-protein interactions--from hot spots to hot segments. Curr Opin Chem Biol 17:952-9.

London, Raveh, Schueler-Furman (2013).
Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how. Curr Opin Struct Biol 23:894-902.

Kilambi, Pacella, Xu, Labonte, Porter, Muthu, Drew, Kuroda, Schueler-Furman, Bonneau, Gray (2013).
Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27. Proteins 81:2201-9.

Lavi, Ngan, Movshovitz-Attias, Bohnuud, Yueh, Beglov, Schueler-Furman, Kozakov (2013).
Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions. Proteins 81:2096-105.

Drayman, Glick, Ben-nun-shaul, Zer, Zlotnick, Gerber, Schueler-Furman, Oppenheim (2013).
Pathogens use structural mimicry of native host ligands as a mechanism for host receptor engagement. Cell Host Microbe 14:63-73.

Chan, Grossman, Zuckerman, Campigli Di Giammartino, Moshel, Scheffner, Monahan, Pilling, Jiang, Haupt, Schueler-Furman, Haupt (2013).
c-Abl phosphorylates E6AP and regulates its E3 ubiquitin ligase activity. Biochemistry 52:3119-29.

Burak, Yogev, Sheffer, Schueler-Furman, Pines (2013).
Evolving dual targeting of a prokaryotic protein in yeast. Mol Biol Evol 30:1563-73.


London, Gulla, Keating & Schueler-Furman (2012).
In-silico and in-vitro elucidation of BH3 binding specificity towards Bcl-2. Biochemistry 51:5841-50.

Brenke, Hall, Chuang, Comeau, Bohnuud, Beglov, Schueler-Furman, Vajada & Kozakov (2012).
Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics. 2012;28:2608-14.

London, Raveh & Schueler-Furman (2012).
Modeling peptide-protein interactions. Methods Mol Biol. 2012;857:375-98.

Slutzky, Barak, Reshef, Schueler-Furman, Lamed & Bayer (2012).
Measurements of relative binding of cohesin and dockerin mutants using an advanced ELISA technique for high-affinity interactions. Methods Enzymol. 510:417-28.

Slutzki, Barak, Reshef, Schueler-Furman, Lamed & Bayer (2012).
Indirect ELISA-based approach for comparative measurement of high-affinity cohesin-dockerin interactions. J Mol Recognit. 2012;25:616-22.

Wexselblatt, Oppenheimer-Shaanan, Kaspy, London, Schueler-Furman, Yavin, Glaser, Katzhendler & Ben-Yehuda (2012).
Relacin, a Novel Antibacterial Agent Targeting the Stringent Response. PLoS Pathog 8:e1002925.


London, Lamphear, Hougland, Fierke & Schueler-Furman (2011).
Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity. PLoS Comput Biol 7:e1002170.

Al-Quadan, Price, London, Schueler-Furman & Abukwaik (2011).
Anchoring of bacterial effectors to host membranes through host-mediated lipidation by prenylation: a common paradigm. Trends Microbiol. 19:573-79.

London, Raveh, Cohen, Fathi & Schueler-Furman (2011).
Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions.Nucleic Acids Res 39(Web Server issue):W249-53.

Raveh, London, Zimmerman & Schueler-Furman (2011).
Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors. PLoS One 6:e18934.

Belitsky, Avshalom, Erental, Yelin, Kumar, London, Sperber, Schueler-Furman & Engelberg-Kulka. (2011).
The Escherichia coli extracellular death factor EDF induces the endoribonucleolytic activities of the toxins MazF and ChpBK. Mol Cell 41:625-35.

Crawley, Gharaei, Ye, Yang, Raveh B, London, Schueler-Furman, Jia, Côté (2011).
Autophosphorylation activates Dictyostelium myosin II heavy chain kinase A by providing a ligand for an allosteric binding site in the alpha-kinase domain. J Biol Chem 286:2607-16.


London, Movshovitz-Attias & Schueler-Furman (2010).
The structural basis of peptide-protein binding strategies.Structure 8:188-199.
Raveh*, London* & Schueler-Furman (2010).
Sub-angstrom Modeling of Complexes between Flexible Peptides and Globular Proteins. Proteins 78:2029-2040.
London*, Raveh*, Movshovitz-Attias & Schueler-Furman (2010).
Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions? Proteins 78:3140-3149.
Reshef, Itzhaki & Schueler-Furman (2010).
Enrichment of highly-conserved domain repeats in prokaryotic proteins. Trends in Genetics 26:383-387.
Movshovitz-Attias, London & Schueler-Furman (2010).
On the use of structural templates for high-resolution docking. Proteins 78:1939-1949.
Kanarek, London, Schueler-Furman & Ben-Neriah (2010).
Ubiquitination and degradation of the inhibitors of NF-kappaB. Cold Spring Harb Perspect Biol.a000166.


Raveh*, Enosh*, Schueler-Furman & Halperin (2009).
Rapid Sampling of Molecular Motions with Prior Information Constraints. PLoS Comput Biol 5:e1000295.
Ben-nun-Shaul, Bronfeld, Reshef, Schueler-Furman & Oppenheim (2009).
The SV40 capsid is stabilized by a conserved pentapeptide hinge of the major capsid protein VP1. J Mol Biol 386:1382-1391.
Dassa, London, Stoddard, Schueler-Furman & Pietrokovsky (2009).
Fractured genes: A novel genomic arrangement involving new split inteins and homing endonuclease family. NAR 37:2560-2573.


London & Schueler-Furman (2008).
Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels. Structure 16:269-279.
London & Schueler-Furman (2008).
FunHunt: Model selection based on energy landscape characteristics. Biochem Soc T. 36:1418-1421.
Enosh*, Raveh*, Furman-Schueler, Halperin & Ben-Tal (2008).
A framework for exploring conformational changes: Application to the transition between the open and closed states of K-channels. Biophys J 95:3850-3860.
Kosakov, Schueler-Furman & Vajda. (2008).
Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins 72:993-1004.
Yanover, Schueler-Furman & Weiss (2008).
Minimizing and learning energy functions for side chain prediction. J Comput Biol 15:899-911.


London N and Schueler-Furman O (2007).
Assessing the energy landscape of CAPRI targets by FunHunt. Proteins 69:809-815.
Wang C*, Schueler-Furman O*, Andre I, London N, Fleishman SJ, Bradley P, Qian B and Baker D. (2007).
RosettaDock in CAPRI rounds 6-12. Proteins 69:758-763. (* equal contribution).
Dassa B, Amitai G, Caspi J, Schueler-Furman O and Pietrokovski S. (2007).
Trans protein splicing of cyanobacterial split inteins in endogenous and exogenous combinations. Biochemistry 46:322-330.


Jojic N, Reyes-Gomez M, Heckerman D, Kadie C and Schueler-Furman O. (2006).
Learning MHC I - peptide binding. Bioinformatics 22: e227-235.
Levy C, Lee Y-N, Nechushtan H, Schueler-Furman O, Sonnenblick A, Hacohen S and Razin E (2006).
Identifying a common molecular mechanism for inhibition of MITF and STAT3 by PIAS3. Blood 107:2839-2845.
Schueler-Furman O, Glick E, Segovia J and Linial M (2006).
Is GAS1 a co-receptor for the GDNF family of ligands? Trends Pharmacol Sci 27:72-77.

Previous representative publications by Ora Schueler-Furman

Schueler-Furman O, Wang C, Bradley P, Misura K and Baker D. (2005).
Progress in modeling of protein structures and interactions. Science 310:638-642.
Schueler-Furman O*, Wang C* and Baker D. (2005).
Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side chain flexibility. Proteins 60:187-194.
Wang C*, Schueler-Furman O* and Baker D. (2005).
Improved side-chain modeling for protein-protein docking. Protein Science 14:1328-1339.
Schueler-Furman O and Baker D. (2003).
Conserved residue clustering and protein structure prediction. Proteins 52:225-235.
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA and Baker D. (2003).
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331:281-299.
Schueler-Furman O, Altuvia Y, Sette A and Margalit H. (2000).
Structure-based prediction of binding peptides to MHC class I molecules: Application to a broad range of MHC alleles. Protein Science 9:1838-1846.
Schueler-Furman O, Elber R and Margalit H. (1998).
Knowledge-based structure prediction of MHC class I bound peptides: A study of twenty-three complexes. Folding & Design 3:549-564.
Altuvia Y, Schueler O and Margalit H. (1995).
Ranking potential binding peptides to MHC molecules by a computational threading approach. J. Mol. Biol. 249: 244-250.
Schueler O and Margalit H. (1995).
Conservation of salt bridges in protein families. J. Mol. Biol. 248: 125-135.