Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 33

1.

Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores.

Ben-David M, Huang H, Sun MGF, Corbi-Verge C, Petsalaki E, Liu K, Gfeller D, Garg P, Tempel W, Sochirca I, Shifman JM, Davidson A, Min J, Kim PM, Sidhu SS.

J Mol Biol. 2019 Jan 18;431(2):336-350. doi: 10.1016/j.jmb.2018.11.018. Epub 2018 Nov 22.

PMID:
30471255
2.

Converting a broad matrix metalloproteinase family inhibitor into a specific inhibitor of MMP-9 and MMP-14.

Shirian J, Arkadash V, Cohen I, Sapir T, Radisky ES, Papo N, Shifman JM.

FEBS Lett. 2018 Apr;592(7):1122-1134. doi: 10.1002/1873-3468.13016. Epub 2018 Mar 12.

3.

Analysis of Structural Features Contributing to Weak Affinities of Ubiquitin/Protein Interactions.

Cohen A, Rosenthal E, Shifman JM.

J Mol Biol. 2017 Nov 10;429(22):3353-3362. doi: 10.1016/j.jmb.2017.09.003. Epub 2017 Sep 11. Review.

PMID:
28911847
4.

Editorial overview: Engineering and design: New trends in designer proteins.

Shifman JM, Papo N.

Curr Opin Struct Biol. 2017 Aug;45:iv-vi. doi: 10.1016/j.sbi.2017.03.001. Epub 2017 Mar 15. No abstract available.

PMID:
28314629
5.

Development of High Affinity and High Specificity Inhibitors of Matrix Metalloproteinase 14 through Computational Design and Directed Evolution.

Arkadash V, Yosef G, Shirian J, Cohen I, Horev Y, Grossman M, Sagi I, Radisky ES, Shifman JM, Papo N.

J Biol Chem. 2017 Feb 24;292(8):3481-3495. doi: 10.1074/jbc.M116.756718. Epub 2017 Jan 13.

6.

Identifying Residues that Determine SCF Molecular-Level Interactions through a Combination of Experimental and In silico Analyses.

Rabinovich E, Heyne M, Bakhman A, Kosloff M, Shifman JM, Papo N.

J Mol Biol. 2017 Jan 6;429(1):97-114. doi: 10.1016/j.jmb.2016.11.018. Epub 2016 Nov 25.

PMID:
27890784
7.

Cold Spots in Protein Binding.

Shirian J, Sharabi O, Shifman JM.

Trends Biochem Sci. 2016 Sep;41(9):739-745. doi: 10.1016/j.tibs.2016.07.002. Epub 2016 Jul 29.

PMID:
27477052
8.

Saturation scanning of ubiquitin variants reveals a common hot spot for binding to USP2 and USP21.

Leung I, Dekel A, Shifman JM, Sidhu SS.

Proc Natl Acad Sci U S A. 2016 Aug 2;113(31):8705-10. doi: 10.1073/pnas.1524648113. Epub 2016 Jul 19.

9.

Protein Engineering by Combined Computational and In Vitro Evolution Approaches.

Rosenfeld L, Heyne M, Shifman JM, Papo N.

Trends Biochem Sci. 2016 May;41(5):421-433. doi: 10.1016/j.tibs.2016.03.002. Epub 2016 Apr 6. Review.

PMID:
27061494
10.

RAS/Effector Interactions from Structural and Biophysical Perspective.

Erijman A, Shifman JM.

Mini Rev Med Chem. 2016;16(5):370-5. Review.

PMID:
26423700
11.

Combinatorial and Computational Approaches to Identify Interactions of Macrophage Colony-stimulating Factor (M-CSF) and Its Receptor c-FMS.

Rosenfeld L, Shirian J, Zur Y, Levaot N, Shifman JM, Papo N.

J Biol Chem. 2015 Oct 23;290(43):26180-93. doi: 10.1074/jbc.M115.671271. Epub 2015 Sep 10.

12.

Synthetic peptides mimicking the binding site of human acetylcholinesterase for its inhibitor fasciculin 2.

Kafurke U, Erijman A, Aizner Y, Shifman JM, Eichler J.

J Pept Sci. 2015 Sep;21(9):723-30. doi: 10.1002/psc.2797. Epub 2015 Jul 22.

PMID:
26200472
13.

How structure defines affinity in protein-protein interactions.

Erijman A, Rosenthal E, Shifman JM.

PLoS One. 2014 Oct 16;9(10):e110085. doi: 10.1371/journal.pone.0110085. eCollection 2014.

14.

Alteration of the C-terminal ligand specificity of the erbin PDZ domain by allosteric mutational effects.

Murciano-Calles J, McLaughlin ME, Erijman A, Hooda Y, Chakravorty N, Martinez JC, Shifman JM, Sidhu SS.

J Mol Biol. 2014 Oct 23;426(21):3500-8. doi: 10.1016/j.jmb.2014.05.003. Epub 2014 May 9.

PMID:
24813123
15.

A single-tube assembly of DNA using the transfer-PCR (TPCR) platform.

Erijman A, Shifman JM, Peleg Y.

Methods Mol Biol. 2014;1116:89-101. doi: 10.1007/978-1-62703-764-8_7.

PMID:
24395359
16.

Predicting affinity- and specificity-enhancing mutations at protein-protein interfaces.

Sharabi O, Shirian J, Shifman JM.

Biochem Soc Trans. 2013 Oct;41(5):1166-9. doi: 10.1042/BST20130121. Review.

PMID:
24059503
17.

Computational methods for controlling binding specificity.

Sharabi O, Erijman A, Shifman JM.

Methods Enzymol. 2013;523:41-59. doi: 10.1016/B978-0-12-394292-0.00003-5.

PMID:
23422425
18.

Transfer-PCR (TPCR): a highway for DNA cloning and protein engineering.

Erijman A, Dantes A, Bernheim R, Shifman JM, Peleg Y.

J Struct Biol. 2011 Aug;175(2):171-7. doi: 10.1016/j.jsb.2011.04.005. Epub 2011 Apr 15.

PMID:
21515384
19.

Triathlon for energy functions: who is the winner for design of protein-protein interactions?

Sharabi O, Dekel A, Shifman JM.

Proteins. 2011 May;79(5):1487-98. doi: 10.1002/prot.22977. Epub 2011 Mar 1.

PMID:
21365678
20.

Multispecific recognition: mechanism, evolution, and design.

Erijman A, Aizner Y, Shifman JM.

Biochemistry. 2011 Feb 8;50(5):602-11. doi: 10.1021/bi101563v. Epub 2011 Jan 13. Review.

PMID:
21229991
21.

Optimizing energy functions for protein-protein interface design.

Sharabi O, Yanover C, Dekel A, Shifman JM.

J Comput Chem. 2011 Jan 15;32(1):23-32. doi: 10.1002/jcc.21594.

PMID:
20623647
22.

What makes Ras an efficient molecular switch: a computational, biophysical, and structural study of Ras-GDP interactions with mutants of Raf.

Filchtinski D, Sharabi O, Rüppel A, Vetter IR, Herrmann C, Shifman JM.

J Mol Biol. 2010 Jun 11;399(3):422-35. doi: 10.1016/j.jmb.2010.03.046. Epub 2010 Mar 31.

PMID:
20361980
23.

Tradeoff between stability and multispecificity in the design of promiscuous proteins.

Fromer M, Shifman JM.

PLoS Comput Biol. 2009 Dec;5(12):e1000627. doi: 10.1371/journal.pcbi.1000627. Epub 2009 Dec 24.

24.

Design, expression and characterization of mutants of fasciculin optimized for interaction with its target, acetylcholinesterase.

Sharabi O, Peleg Y, Mashiach E, Vardy E, Ashani Y, Silman I, Sussman JL, Shifman JM.

Protein Eng Des Sel. 2009 Oct;22(10):641-8. doi: 10.1093/protein/gzp045. Epub 2009 Jul 30.

25.

Intricacies of Beta sheet protein design.

Shifman JM.

Structure. 2008 Dec 10;16(12):1751-2. doi: 10.1016/j.str.2008.11.001. No abstract available.

26.

Computational design of calmodulin mutants with up to 900-fold increase in binding specificity.

Yosef E, Politi R, Choi MH, Shifman JM.

J Mol Biol. 2009 Feb 6;385(5):1470-80. doi: 10.1016/j.jmb.2008.09.053. Epub 2008 Sep 27.

PMID:
18845160
27.

Dead-end elimination for multistate protein design.

Yanover C, Fromer M, Shifman JM.

J Comput Chem. 2007 Oct;28(13):2122-9.

PMID:
17471460
28.

Ca2+/calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums.

Shifman JM, Choi MH, Mihalas S, Mayo SL, Kennedy MB.

Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):13968-73. Epub 2006 Sep 11.

29.

Exploring the origins of binding specificity through the computational redesign of calmodulin.

Shifman JM, Mayo SL.

Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13274-9. Epub 2003 Nov 3.

30.

Modulating calmodulin binding specificity through computational protein design.

Shifman JM, Mayo SL.

J Mol Biol. 2002 Oct 25;323(3):417-23.

PMID:
12381298
31.

Heme redox potential control in de novo designed four-alpha-helix bundle proteins.

Shifman JM, Gibney BR, Sharp RE, Dutton PL.

Biochemistry. 2000 Dec 5;39(48):14813-21.

PMID:
11101297
32.

Computational design of an integrin I domain stabilized in the open high affinity conformation.

Shimaoka M, Shifman JM, Jing H, Takagi J, Mayo SL, Springer TA.

Nat Struct Biol. 2000 Aug;7(8):674-8.

PMID:
10932253
33.

Functionalized de novo designed proteins: mechanism of proton coupling to oxidation/reduction in heme protein maquettes.

Shifman JM, Moser CC, Kalsbeck WA, Bocian DF, Dutton PL.

Biochemistry. 1998 Nov 24;37(47):16815-27.

PMID:
9843452

Supplemental Content

Loading ...
Support Center