List of Publications

2011

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.

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.

2010

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.

2009

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.

2008

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.

2007

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.

2006

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.