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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