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Items: 1 to 50 of 103

1.

SnapDock-template-based docking by Geometric Hashing.

Estrin M, Wolfson HJ.

Bioinformatics. 2017 Jul 15;33(14):i30-i36. doi: 10.1093/bioinformatics/btx233.

2.

Protein-Peptide Interaction Design: PepCrawler and PinaColada.

Zaidman D, Wolfson HJ.

Methods Mol Biol. 2017;1561:279-290. doi: 10.1007/978-1-4939-6798-8_16.

PMID:
28236244
3.

Memdock: an α-helical membrane protein docking algorithm.

Hurwitz N, Schneidman-Duhovny D, Wolfson HJ.

Bioinformatics. 2016 Aug 15;32(16):2444-50. doi: 10.1093/bioinformatics/btw184. Epub 2016 Apr 8.

PMID:
27153621
4.

PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm.

Zaidman D, Wolfson HJ.

Bioinformatics. 2016 Aug 1;32(15):2289-96. doi: 10.1093/bioinformatics/btw133. Epub 2016 Mar 11.

PMID:
27153578
5.

DockStar: a novel ILP-based integrative method for structural modeling of multimolecular protein complexes.

Amir N, Cohen D, Wolfson HJ.

Bioinformatics. 2015 Sep 1;31(17):2801-7. doi: 10.1093/bioinformatics/btv270. Epub 2015 Apr 25.

PMID:
25913207
6.

Novel LIMK2 Inhibitor Blocks Panc-1 Tumor Growth in a mouse xenograft model.

Rak R, Haklai R, Elad-Tzfadia G, Wolfson HJ, Carmeli S, Kloog Y.

Oncoscience. 2014 Jan 1;1(1):39-48. eCollection 2014.

7.

Blind prediction of interfacial water positions in CAPRI.

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ.

Proteins. 2014 Apr;82(4):620-32. doi: 10.1002/prot.24439. Epub 2013 Nov 23.

8.

Conformational transitions in human translin enable nucleic acid binding.

Pérez-Cano L, Eliahoo E, Lasker K, Wolfson HJ, Glaser F, Manor H, Bernadó P, Fernández-Recio J.

Nucleic Acids Res. 2013 Nov;41(21):9956-66. doi: 10.1093/nar/gkt765. Epub 2013 Aug 26.

9.

Diameter-selective dispersion of carbon nanotubes by β-lactoglobulin whey protein.

Karchemsky F, Drug E, Mashiach-Farkash E, Fadeev L, Wolfson HJ, Gozin M, Regev O.

Colloids Surf B Biointerfaces. 2013 Dec 1;112:16-22. doi: 10.1016/j.colsurfb.2013.07.018. Epub 2013 Jul 16.

PMID:
23933103
10.

Structure-based in silico identification of ubiquitin-binding domains provides insights into the ALIX-V:ubiquitin complex and retrovirus budding.

Keren-Kaplan T, Attali I, Estrin M, Kuo LS, Farkash E, Jerabek-Willemsen M, Blutraich N, Artzi S, Peri A, Freed EO, Wolfson HJ, Prag G.

EMBO J. 2013 Feb 20;32(4):538-51. doi: 10.1038/emboj.2013.4. Epub 2013 Jan 29.

11.

Computer-based identification of a novel LIMK1/2 inhibitor that synergizes with salirasib to destabilize the actin cytoskeleton.

Mashiach-Farkash E, Rak R, Elad-Sfadia G, Haklai R, Carmeli S, Kloog Y, Wolfson HJ.

Oncotarget. 2012 Jun;3(6):629-39.

12.

PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors.

Donsky E, Wolfson HJ.

Bioinformatics. 2011 Oct 15;27(20):2836-42. doi: 10.1093/bioinformatics/btr498. Epub 2011 Aug 31.

PMID:
21880702
13.

ParaDock: a flexible non-specific DNA--rigid protein docking algorithm.

Banitt I, Wolfson HJ.

Nucleic Acids Res. 2011 Nov 1;39(20):e135. doi: 10.1093/nar/gkr620. Epub 2011 Aug 10.

14.

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.

Tjioe E, Lasker K, Webb B, Wolfson HJ, Sali A.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W167-70. doi: 10.1093/nar/gkr490.

15.

SymmRef: a flexible refinement method for symmetric multimers.

Mashiach-Farkash E, Nussinov R, Wolfson HJ.

Proteins. 2011 Sep;79(9):2607-23. doi: 10.1002/prot.23082. Epub 2011 Jun 30.

16.

Protein structure prediction using a docking-based hierarchical folding scheme.

Kifer I, Nussinov R, Wolfson HJ.

Proteins. 2011 Jun;79(6):1759-73. doi: 10.1002/prot.22999. Epub 2011 Mar 28.

17.

GOSSIP: a method for fast and accurate global alignment of protein structures.

Kifer I, Nussinov R, Wolfson HJ.

Bioinformatics. 2011 Apr 1;27(7):925-32. doi: 10.1093/bioinformatics/btr044. Epub 2011 Feb 3.

18.

Symmetry-based self-assembled nanotubes constructed using native protein structures: the key role of flexible linkers.

Buch I, Tsai CJ, Wolfson HJ, Nussinov R.

Protein Pept Lett. 2011 Apr;18(4):362-72.

PMID:
21222638
19.

Allosteric regulation of glycogen synthase kinase 3β: a theoretical study.

Buch I, Fishelovitch D, London N, Raveh B, Wolfson HJ, Nussinov R.

Biochemistry. 2010 Dec 28;49(51):10890-901. doi: 10.1021/bi100822q. Epub 2010 Dec 3.

20.

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map.

Lasker K, Sali A, Wolfson HJ.

Proteins. 2010 Nov 15;78(15):3205-11. doi: 10.1002/prot.22845.

21.

An integrated suite of fast docking algorithms.

Mashiach E, Schneidman-Duhovny D, Peri A, Shavit Y, Nussinov R, Wolfson HJ.

Proteins. 2010 Nov 15;78(15):3197-204. doi: 10.1002/prot.22790.

22.

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking.

Mashiach E, Nussinov R, Wolfson HJ.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W457-61. doi: 10.1093/nar/gkq373. Epub 2010 May 11.

23.

How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel?

Fishelovitch D, Shaik S, Wolfson HJ, Nussinov R.

J Phys Chem B. 2010 May 6;114(17):5964-70. doi: 10.1021/jp101894k.

24.

FiberDock: Flexible induced-fit backbone refinement in molecular docking.

Mashiach E, Nussinov R, Wolfson HJ.

Proteins. 2010 May 1;78(6):1503-19. doi: 10.1002/prot.22668.

25.

Novel approach for efficient pharmacophore-based virtual screening: method and applications.

Dror O, Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ.

J Chem Inf Model. 2009 Oct;49(10):2333-43. doi: 10.1021/ci900263d.

26.
27.

Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly.

Lasker K, Topf M, Sali A, Wolfson HJ.

J Mol Biol. 2009 Apr 24;388(1):180-94. doi: 10.1016/j.jmb.2009.02.031. Epub 2009 Feb 20.

28.

Computational validation of protein nanotubes.

Buch I, Brooks BR, Wolfson HJ, Nussinov R.

Nano Lett. 2009 Mar;9(3):1096-102. doi: 10.1021/nl803521j.

29.

Self-assembly of fused homo-oligomers to create nanotubes.

Buch I, Tsai CJ, Wolfson HJ, Nussinov R.

Methods Mol Biol. 2008;474:117-31. doi: 10.1007/978-1-59745-480-3_8. Review.

PMID:
19031064
30.

RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases.

Shulman-Peleg A, Nussinov R, Wolfson HJ.

Nucleic Acids Res. 2009 Jan;37(Database issue):D369-73. doi: 10.1093/nar/gkn759. Epub 2008 Oct 25.

31.

Analysis and classification of RNA tertiary structures.

Abraham M, Dror O, Nussinov R, Wolfson HJ.

RNA. 2008 Nov;14(11):2274-89. doi: 10.1261/rna.853208. Epub 2008 Sep 29.

32.

Structural similarity of genetically interacting proteins.

Dror O, Schneidman-Duhovny D, Shulman-Peleg A, Nussinov R, Wolfson HJ, Sharan R.

BMC Syst Biol. 2008 Jul 31;2:69. doi: 10.1186/1752-0509-2-69.

33.

Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules.

Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ.

J Comput Biol. 2008 Sep;15(7):737-54. doi: 10.1089/cmb.2007.0130.

34.

Principles of flexible protein-protein docking.

Andrusier N, Mashiach E, Nussinov R, Wolfson HJ.

Proteins. 2008 Nov 1;73(2):271-89. doi: 10.1002/prot.22170. Review.

35.

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions.

Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W260-4. doi: 10.1093/nar/gkn185. Epub 2008 May 8.

36.

Prediction of interacting single-stranded RNA bases by protein-binding patterns.

Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ.

J Mol Biol. 2008 May 30;379(2):299-316. doi: 10.1016/j.jmb.2008.03.043. Epub 2008 Mar 28.

37.

MolAxis: a server for identification of channels in macromolecules.

Yaffe E, Fishelovitch D, Wolfson HJ, Halperin D, Nussinov R.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W210-5. doi: 10.1093/nar/gkn223. Epub 2008 Apr 29.

38.

Constructing templates for protein structure prediction by simulation of protein folding pathways.

Kifer I, Nussinov R, Wolfson HJ.

Proteins. 2008 Nov 1;73(2):380-94. doi: 10.1002/prot.22073.

39.

PharmaGist: a webserver for ligand-based pharmacophore detection.

Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W223-8. doi: 10.1093/nar/gkn187. Epub 2008 Apr 19.

40.

FireDock: a web server for fast interaction refinement in molecular docking.

Mashiach E, Schneidman-Duhovny D, Andrusier N, Nussinov R, Wolfson HJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W229-32. doi: 10.1093/nar/gkn186. Epub 2008 Apr 19.

41.

MolAxis: efficient and accurate identification of channels in macromolecules.

Yaffe E, Fishelovitch D, Wolfson HJ, Halperin D, Nussinov R.

Proteins. 2008 Oct;73(1):72-86. doi: 10.1002/prot.22052.

42.

Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment.

Shatsky M, Nussinov R, Wolfson HJ.

Methods Mol Biol. 2008;413:125-46.

PMID:
18075164
43.

QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding.

Fishelovitch D, Hazan C, Hirao H, Wolfson HJ, Nussinov R, Shaik S.

J Phys Chem B. 2007 Dec 13;111(49):13822-32. Epub 2007 Nov 17.

44.

Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: In silico predictions and experimental validation.

Julsing MK, Vasilev NP, Schneidman-Duhovny D, Muntendam R, Woerdenbag HJ, Quax WJ, Wolfson HJ, Ionkova I, Kayser O.

Eur J Med Chem. 2008 Jun;43(6):1171-9. Epub 2007 Sep 19.

PMID:
17998150
45.

Spatial chemical conservation of hot spot interactions in protein-protein complexes.

Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ.

BMC Biol. 2007 Oct 9;5:43.

46.

Automatic prediction of protein interactions with large scale motion.

Schneidman-Duhovny D, Nussinov R, Wolfson HJ.

Proteins. 2007 Dec 1;69(4):764-73.

PMID:
17886339
47.

HingeProt: automated prediction of hinges in protein structures.

Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T.

Proteins. 2008 Mar;70(4):1219-27.

PMID:
17847101
48.

Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit.

Miled N, Yan Y, Hon WC, Perisic O, Zvelebil M, Inbar Y, Schneidman-Duhovny D, Wolfson HJ, Backer JM, Williams RL.

Science. 2007 Jul 13;317(5835):239-42.

49.

FireDock: fast interaction refinement in molecular docking.

Andrusier N, Nussinov R, Wolfson HJ.

Proteins. 2007 Oct 1;69(1):139-59.

PMID:
17598144
50.

Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4.

Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R.

J Am Chem Soc. 2007 Feb 14;129(6):1602-11.

PMID:
17284003

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