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Nurit Haspel - Publications

Affiliations: 
Computer Science University of Massachusetts, Boston, Boston, MA 
Area:
Computer Science, Bioinformatics Biology, Molecular Biology
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Afrasiabi F, Dehghanpoor R, Haspel N. Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC. Molecules (Basel, Switzerland). 26. PMID 33923805 DOI: 10.3390/molecules26082329  0.34
2021 Campbell KL, Haspel N, Gath C, Kurniatash N, Nouduri Akkiraju I, Stuffers N, Vadher U. Protein Hormone Fragmentation in Intercellular Signaling: Hormones as Nested Information Systems†. Biology of Reproduction. PMID 33403392 DOI: 10.1093/biolre/ioaa234  0.323
2020 Haspel N, Jang H, Nussinov R. Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics. Biophysical Journal. PMID 33347888 DOI: 10.1016/j.bpj.2020.12.007  0.387
2019 Vajdi A, Zarringhalam K, Haspel N. Patch-DCA: Improved Protein Interface Prediction by utilizing Structural Information and Clustering DCA scores. Bioinformatics (Oxford, England). PMID 31621841 DOI: 10.1093/Bioinformatics/Btz791  0.736
2019 Joshi A, Haspel N. Clustering of Protein Conformations Using Parallelized Dimensionality Reduction Journal of Advances in Information Technology. 10: 142-147. DOI: 10.12720/Jait.10.4.142-147  0.677
2018 Dehghanpoor R, Ricks E, Hursh K, Gunderson S, Farhoodi R, Haspel N, Hutchinson B, Jagodzinski F. Predicting the Effect of Single and Multiple Mutations on Protein Structural Stability. Molecules (Basel, Switzerland). 23. PMID 29382060 DOI: 10.3390/Molecules23020251  0.362
2017 Haspel N, Luo D, González E. Detecting intermediate protein conformations using algebraic topology. Bmc Bioinformatics. 18: 502. PMID 29244007 DOI: 10.1186/S12859-017-1918-Z  0.414
2017 Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods in Molecular Biology (Clifton, N.J.). 1529: 323-352. PMID 27914060 DOI: 10.1007/978-1-4939-6637-0_17  0.509
2017 Haspel N, Jagodzinski F. Methods for Detecting Critical Residues in Proteins. Methods in Molecular Biology (Clifton, N.J.). 1498: 227-242. PMID 27709579 DOI: 10.1007/978-1-4939-6472-7_15  0.446
2016 Farhoodi R, Akbal-Delibas B, Haspel N. Machine Learning Approaches for Predicting Protein Complex Similarity. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27748625 DOI: 10.1089/Cmb.2016.0137  0.417
2016 Vajdi A, Haspel N. Clustering protein conformations using a dynamic programming based similarity measurement Proceedings of the 8th International Conference On Bioinformatics and Computational Biology, Bicob 2016. 31-36.  0.378
2015 Akbal-Delibas B, Farhoodi R, Pomplun M, Haspel N. Accurate refinement of docked protein complexes using evolutionary information and deep learning. Journal of Bioinformatics and Computational Biology. 1642002. PMID 26846813 DOI: 10.1142/S0219720016420026  0.376
2015 Akbal-Delibas B, Pomplun M, Haspel N. Accurate Prediction of Docked Protein Structure Similarity. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 892-904. PMID 26335807 DOI: 10.1089/Cmb.2015.0114  0.429
2015 Vajdi A, Haspel N, Banaee H. A new DP algorithm for comparing gene expression data using geometrics similarity Proceedings - 2015 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2015. 1745-1747. DOI: 10.1109/BIBM.2015.7359948  0.693
2015 Vajdi A, Haspel N, Banaee H. A new DP algorithm for comparing gene expression data using geometric similarity Proceedings - 2015 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2015. 1157-1161. DOI: 10.1109/BIBM.2015.7359846  0.693
2015 Akbal-Delibas B, Pomplun M, Haspel N. AccuRefiner: A machine learning guided refinement method for protein-protein docking Proceedings of the 7th International Conference On Bioinformatics and Computational Biology, Bicob 2015. 125-130.  0.307
2014 Akbal-Delibas B, Pomplun M, Haspel N. Accu RMSD: A machine learning approach to predicting structure similarity of docked protein complexes Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 289-296. DOI: 10.1145/2649387.2649392  0.327
2014 Murase SK, Haspel N, Del Valle LJ, Perpète EA, Michaux C, Nussinov R, Puiggalí J, Alemán C. Molecular characterization of l-phenylalanine terminated poly(l-lactide) conjugates Rsc Advances. 4: 23231-23241. DOI: 10.1039/C4Ra01534G  0.459
2013 Akbal-Delibas B, Haspel N. A conservation and biophysics guided stochastic approach to refining docked multimeric proteins. Bmc Structural Biology. 13: S7. PMID 24565106 DOI: 10.1186/1472-6807-13-S1-S7  0.399
2013 Akbal-Delibas B, Jagodzinski F, Haspel N. A conservation and rigidity based method for detecting critical protein residues. Bmc Structural Biology. 13: S6. PMID 24565061 DOI: 10.1186/1472-6807-13-S1-S6  0.45
2013 He J, Shehu A, Haspel N, Chen B. The 6th Computational Structural Bioinformatics Workshop. Bmc Structural Biology. 13: I1. PMID 24564893 DOI: 10.1186/1472-6807-13-S1-I1  0.467
2013 Zanuy D, Kotla R, Nussinov R, Teesalu T, Sugahara KN, Alemán C, Haspel N. Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor. Journal of Structural Biology. 182: 78-86. PMID 23462097 DOI: 10.1016/J.Jsb.2013.02.006  0.462
2013 Luo D, Haspel N. Multi-resolution rigidity-based sampling of protein conformational paths 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 786-792. DOI: 10.1145/2506583.2506710  0.375
2013 Jagodzinski F, Akbal-Delibas B, Haspel N. An evolutionary conservation & rigidity analysis machine learning approach for detecting critical protein residues 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 779-785. DOI: 10.1145/2506583.2506708  0.348
2013 Vetro R, Haspel N, Simovici D. Characterizing intermediate conformations in protein conformational space Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7845: 70-80. DOI: 10.1007/978-3-642-38342-7_7  0.333
2013 Haspel N, Luo D, González E. Detecting intermediate structures in protein conformational pathways 5th International Conference On Bioinformatics and Computational Biology 2013, Bicob 2013. 47-52.  0.363
2012 Haspel N, Laurent AD, Zanuy D, Nussinov R, Alemán C, Puiggalí J, Revilla-López G. Conformational exploration of two peptides and their hybrid polymer conjugates: potentialities as self-aggregating materials. The Journal of Physical Chemistry. B. 116: 13941-52. PMID 23157485 DOI: 10.1021/Jp3043363  0.468
2012 Hashmi I, Akbal-Delibas B, Haspel N, Shehu A. Guiding protein docking with geometric and evolutionary information. Journal of Bioinformatics and Computational Biology. 10: 1242008. PMID 22809384 DOI: 10.1142/S0219720012420085  0.433
2012 Akbal-Delibas B, Hashmi I, Shehu A, Haspel N. An evolutionary conservation-based method for refining and reranking protein complex structures. Journal of Bioinformatics and Computational Biology. 10: 1242002. PMID 22809378 DOI: 10.1142/S0219720012420024  0.409
2012 Akbal-Delibas B, Haspel N. An evolutionary-guided iterative refinement approach for protein multimers Proceedings - 2012 Ieee International Conference On Bioinformatics and Biomedicine Workshops, Bibmw 2012. 941. DOI: 10.1109/BIBMW.2012.6470273  0.305
2012 Akbal-Delibas B, Jagodzinski F, Haspel N. Combining conservation and rigidity methods to detect critical residues in proteins Proceedings - 2012 Ieee International Conference On Bioinformatics and Biomedicine Workshops, Bibmw 2012. 940. DOI: 10.1109/BIBMW.2012.6470271  0.345
2012 Akbal-Delibas B, Jagodzinski F, Haspel N. Towards a hybrid method for detecting critical protein residues Proceedings - 2012 Ieee International Conference On Bioinformatics and Biomedicine Workshops, Bibmw 2012. 82-85. DOI: 10.1109/BIBMW.2012.6470240  0.36
2012 Haspel N. Tracing conformational changes in proteins represented at a coarse level Lecture Notes of the Institute For Computer Sciences, Social-Informatics and Telecommunications Engineering. 87: 343-356. DOI: 10.1007/978-3-642-32615-8_34  0.322
2012 Haspel N, González E. Topological properties of the configuration spaces of proteins 4th International Conference On Bioinformatics and Computational Biology 2012, Bicob 2012. 245-250.  0.332
2011 Haspel N, Zanuy D, Nussinov R, Teesalu T, Ruoslahti E, Aleman C. Binding of a C-end rule peptide to the neuropilin-1 receptor: a molecular modeling approach. Biochemistry. 50: 1755-62. PMID 21247217 DOI: 10.1021/Bi101662J  0.471
2011 Hashmi I, Akbal-Delibas B, Haspel N, Shehu A. Protein docking with information on evolutionary conserved interfaces 2011 Ieee International Conference On Bioinformatics and Biomedicine Workshops, Bibmw 2011. 358-365. DOI: 10.1109/BIBMW.2011.6112399  0.354
2010 Haspel N, Moll M, Baker ML, Chiu W, Kavraki LE. Tracing conformational changes in proteins. Bmc Structural Biology. 10: S1. PMID 20487508 DOI: 10.1186/1472-6807-10-S1-S1  0.402
2010 Haspel N, Geisbrecht BV, Lambris J, Kavraki L. Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex. Proteins. 78: 1004-14. PMID 19899169 DOI: 10.1002/Prot.22624  0.426
2009 Zanuy D, Ballano G, Jiménez AI, Casanovas J, Haspel N, Cativiela C, Curcó D, Nussinov R, Alemán C. Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale. Journal of Chemical Information and Modeling. 49: 1623-9. PMID 19548653 DOI: 10.1021/Ci9001487  0.4
2008 Ricklin D, Ricklin-Lichtsteiner SK, Sfyroera G, Chen H, Tzekou A, Magotti P, Wu Y, Garcia BL, McWorther WJ, Haspel N, Kavraki LE, Geisbrecht BV, Lambris JD. Novel insights into target specificities and molecular mechanisms for two potent complement evasion proteins from Staphylococcus aureus Molecular Immunology. 45: 4114-4115. DOI: 10.1016/J.Molimm.2008.08.058  0.329
2008 Haspel N, Zanuy D, Tsai HH, Ma B, Wolfson H, Nussinov R. Computational Approaches and Tools for Establishing Structural Models for Short Amyloid-forming Peptides Amyloid Proteins: the Beta Sheet Conformation and Disease. 1: 301-315. DOI: 10.1002/9783527619344.ch13  0.397
2007 Zanuy D, Rodríguez-Ropero F, Haspel N, Zheng J, Nussinov R, Aleman C. Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences. Biomacromolecules. 8: 3135-46. PMID 17854222 DOI: 10.1021/Bm700561T  0.518
2007 Haspel N, Zanuy D, Zheng J, Aleman C, Wolfson H, Nussinov R. Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer. Biophysical Journal. 93: 245-53. PMID 17416628 DOI: 10.1529/Biophysj.106.100644  0.499
2007 Tsai CJ, Zheng J, Zanuy D, Haspel N, Wolfson H, Alemán C, Nussinov R. Principles of nanostructure design with protein building blocks. Proteins. 68: 1-12. PMID 17407160 DOI: 10.1002/Prot.21413  0.519
2007 Zheng J, Zanuy D, Haspel N, Tsai CJ, Alemán C, Nussinov R. Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues. Biochemistry. 46: 1205-18. PMID 17260950 DOI: 10.1021/Bi061674A  0.547
2007 Haspel N, Wainreb G, Inbar Y, Tsai HH, Tsai CJ, Wolfson HJ, Nussinov R. A hierarchical protein folding scheme based on the building block folding model. Methods in Molecular Biology (Clifton, N.J.). 350: 189-204. PMID 16957324 DOI: 10.1385/1-59745-189-4:189  0.54
2006 Haspel N, Zanuy D, Alemán C, Wolfson H, Nussinov R. De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs. Structure (London, England : 1993). 14: 1137-48. PMID 16843895 DOI: 10.1016/J.Str.2006.05.016  0.537
2006 Alemán C, Zanuy D, Jiménez AI, Cativiela C, Haspel N, Zheng J, Casanovas J, Wolfson H, Nussinov R. Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids. Physical Biology. 3: S54-62. PMID 16582465 DOI: 10.1088/1478-3975/3/1/S06  0.492
2006 Wainreb G, Haspel N, Wolfson HJ, Nussinov R. A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly. Bioinformatics (Oxford, England). 22: 1343-52. PMID 16543273 DOI: 10.1093/Bioinformatics/Btl098  0.553
2005 Haspel N, Zanuy D, Ma B, Wolfson H, Nussinov R. A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core. Journal of Molecular Biology. 345: 1213-27. PMID 15644216 DOI: 10.1016/J.Jmb.2004.11.002  0.483
2004 Zanuy D, Haspel N, Tsai HH, Ma B, Gunasekaran K, Wolfson HJ, Nussinov R. Side chain interactions determine the amyloid organization: a single layer beta-sheet molecular structure of the calcitonin peptide segment 15-19. Physical Biology. 1: 89-99. PMID 16204826 DOI: 10.1088/1478-3967/1/2/005  0.501
2004 Tsai HH, Zanuy D, Haspel N, Gunasekaran K, Ma B, Tsai CJ, Nussinov R. The stability and dynamics of the human calcitonin amyloid peptide DFNKF. Biophysical Journal. 87: 146-58. PMID 15240453 DOI: 10.1529/Biophysj.104.040352  0.467
2003 Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, Benyamini H, Barzilai A, Dror O, Haspel N, Nussinov R, Wolfson HJ. Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins. 52: 107-12. PMID 12784375 DOI: 10.1002/Prot.10397  0.461
2003 Haspel N, Tsai CJ, Wolfson H, Nussinov R. Reducing the computational complexity of protein folding via fragment folding and assembly. Protein Science : a Publication of the Protein Society. 12: 1177-87. PMID 12761388 DOI: 10.1110/Ps.0232903  0.583
2003 Haspel N, Tsai CJ, Wolfson H, Nussinov R. Hierarchical protein folding pathways: a computational study of protein fragments. Proteins. 51: 203-15. PMID 12660989 DOI: 10.1002/Prot.10294  0.55
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