Nurit Haspel's publications

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Classified by Research Category

• Amyloids • Molecular Modeling • Protein Folding • Conformational Search • Docking •

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Amyloids

N., Haspel, D., Zanuy, B., Ma, H., Wolfson, and R., Nussinov. A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: A single beta-sheet model with a small hydrohpobic core.. J Mol Biol., 345(5):1213–1227, 2005.

N., Haspel, D., Zanuy, H.H., Tsai, B., Ma, H., Wolfson, and R., Nussinov. Computational approaches and tools for establishing structural models for short amyloid-forming peptides.. In Amyloid Proteins, pp. 301–318, Ed. Jean D. Sipe.Wiley-VCH, 2005.

H.H., Tsai, D., Zanuy, N., Haspel, K., Gunasekaran, B., Ma, C.J., Tsai, and R. Nussinov. The stability and dynamic of the human Calcitonin amyloid peptide DFNKF.. Biophys. J., 87(1):146–158, 2004.

D., Zanuy, N., Haspel, H.H., Tsai, B., Ma, G., Kannan, H., Wolfson, and R. Nussinov. Side chain interactions determine the amyloid organization: A single layer beta-sheet molecular structure of the calcitonin peptide segment 15-19.. Phys. Biol., 1:89–99, 2004.

Molecular Modeling

N., Haspel, D., Zanuy, R., Nussinov, T., Teesalu, E., Ruoslahti and C. Aleman. Binding of a C-end rule peptide to the neuropilin-1 receptor: a molecular modeling approach.Biomacromolecules, 50(10):1755-1762, 2011.

N., Haspel, B., Geisbrecht, J.D., Lambris, and L.E. Kavraki. Multi-scale Characterization of the Energy Landscape of Proteins with Application to the C3d/Efb-C Complex. Proteins: Structure, Function and Bioinformatics, 78(4):1004-1014, 2010.

D., Zanuy, G., Ballano, A.I., Jimenez AI, J., Casanovas, N., Haspel, C., Cativiela, D., Curco, R., Nussinov and C., Aleman. Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale. Journal of Chemical Information and Modeling, 49(7):1623–1629, 2009.

N., Haspel, D., Ricklin, B., Geisbrecht, J., Lambris, and L.E., Kavraki . Electrostatic Contributions Drive the Interaction Between Staphylococcus aureus Protein Efb-C and its Complement Target C3d. Prot. Sci., 17(11):1894–1906, 2008.

N., Haspel, D., Zanuy, J., Zheng, C., Aleman, H., Wolfson, and R. Nussinov. Changing the charge distribution of beta-helical based nanostructures can provide the conditions for charge transfer. Biophys. J., 93:245–253, 2007.

J.,Zheng, D., Zanuy, N., Haspel, C.J., Tsai, C., Aleman, and R., Nussinov. Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues.. Biochemistry, 46(5):1205–1218, 2007.

D. Zanuy, F. Rodriguez-Ropero, N. Haspel, J. Zheng, R. Nussinov, and C. Aleman. Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences. . Biomacromolecules, 8(10):3135–3146, 2007.

C.J., Tsai, J.,Zheng, D., Zanuy, N., Haspel, and R., Nussinov. Principles of nanostructure design with protein building blocks. Proteins, 68, 2007.

C., Aleman, D., Zanuy, A.I., Jimenez, C., Cativiela, N., Haspel, J., Zheng, J., Casanovas, H., Wolfson, and R., Nussinov. Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids.. Phys. Biol., 3(1):S54–62, 2006.

N., Haspel, D., Zanuy, C., Aleman, H., Wolfson, and Nussinov R.. De-novo tubular nanostructure design based on self-assembly of beta-helical protein motifs.. Structure, 14:1137–1148, 2006.

Protein folding

N., Haspel, G., Wainreb, Y., Inbar, H.H., Tsai, C.J., Tsai, H.J., Wolfson, and R., Nussinov. A hierarchical protein folding scheme based on the building block folding model. Methods Mol. Biol., 350:189–204, 2007.

G., Wainreb, N., Haspel, H., Wolfson, and R., Nussinov. A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly. Bioinformatics, 22:1343–1352, 2006.

N., Haspel, C.J., Tsai, H., Wolfson, and R., Nussinov. Hierarchical protein folding pathways: A computational study of protein fragments.. Proteins, 51:203–215, 2003.

N., Haspel, C.J., Tsai, H., Wolfson, and R., Nussinov. Reducing the computational complexity of protein folding via fragment folding and assembly.. Prot. Sci., 12:1177–1187, 2003.

N., Haspel, C.J., Tsai, H., Wolfson, and R., Nussinov. From the building blocks folding model to protein structure prediction. In Protein Structure Prediction: Bioinformatics approach, pp. 201–226, Ed. Tsigelny I., 2002.

S., Kumar, A., Barzilai, N., Haspel, Y.Y., Sham, C.J., Tsai, H., Wolfson, and R., Nussinov. Critical building blocks in proteins: a common theme in folding and binding. In Recent Research Developments in Protein Folding, Stability and Design., Gromiha, M. KH. and Selvarage, S., Trivadrum, India, 2002.

Conformational search

N., Haspel. Tracing conformational changes in proteins represented at a coarse level. proc. of BIONETICS 2010, Dec. 1-3 2010, Boston MA, USA.

N., Haspel, M., Moll, M.L., Baker, W., Chiu and L.E. Kavraki. Tracing conformational changes in proteins.BMC Structural Biology, 10 Suppl 1 (S1), 2010.

N., Haspel, M., Moll, M.L., Baker, W., Chiu and L.E. Kavraki. Tracing conformational changes in proteins. proceedings of the Computational Structural Biology Workshop (CSBW '09), in conjunction with IEEE international conference on Bioinformatics and Biomedicine (BIBM 09), Washington DC, Nov. 2009.

Docking

B. Akbal, I. Hashmi, A. Shehu and N. Haspel. Refinement of protein complex structures using evolutionary traces.Proc. of the Computational Structural Biology Workshop (CSBW), in conjunction with IEEE BIBM '11, 400-405, 2011.

I. Hashmi, B. Akbal, N. Haspel and A. Shehu. Protein docking with information on evilutionary conserved interfaces.Proc. of the Computational Structural Biology Workshop (CSBW), in conjunction with IEEE BIBM '11, 358-365, 2011.

D. Schneidman-Duhovny, Y. Inbar, V. Polak, M. Shatsky, I. Halperin, H. Benyamini, A. Barzilai, O. Dror, N. Haspel, R. Nussinov, and H.J. Wolfson. Taking geometry to its edge: Fast unbound rigid (and hinge-bent) docking. Proteins, 52(1):107–112, 2003.

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