Shifman JM - Search Results

1

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

Yosef E, Politi R, Choi MH, Shifman JM. Yosef E, et al. Among authors: shifman jm. J Mol Biol. 2009 Feb 6;385(5):1470-80. doi: 10.1016/j.jmb.2008.09.053. Epub 2008 Sep 27. J Mol Biol. 2009. PMID: 18845160

2

ProBASS - a language model with sequence and structural features for predicting the effect of mutations on binding affinity.

Gurusinghe SNS, Wu Y, DeGrado W, Shifman JM. Gurusinghe SNS, et al. Among authors: shifman jm. bioRxiv [Preprint]. 2024 Jun 26:2024.06.21.600041. doi: 10.1101/2024.06.21.600041. bioRxiv. 2024. PMID: 38979193 Free PMC article. Preprint.

3

Improving Circulation Half-Life of Therapeutic Candidate N-TIMP2 by Unfolded Peptide Extension.

Shirian J, Hockla A, Gleba JJ, Coban M, Rotenberg N, Strik LM, Alasonyalilar Demirer A, Pawlush ML, Copland JA, Radisky ES, Shifman JM. Shirian J, et al. Among authors: shifman jm. bioRxiv [Preprint]. 2024 Jun 27:2024.06.27.600979. doi: 10.1101/2024.06.27.600979. bioRxiv. 2024. Update in: Biomolecules. 2024 Sep 20;14(9):1187. doi: 10.3390/biom14091187 PMID: 38979353 Free PMC article. Updated. Preprint.

4

Modulating calmodulin binding specificity through computational protein design.

Shifman JM, Mayo SL. Shifman JM, et al. J Mol Biol. 2002 Oct 25;323(3):417-23. doi: 10.1016/s0022-2836(02)00881-1. J Mol Biol. 2002. PMID: 12381298

5

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. Shifman JM, et al. Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):13968-73. doi: 10.1073/pnas.0606433103. Epub 2006 Sep 11. Proc Natl Acad Sci U S A. 2006. PMID: 16966599 Free PMC article.

6

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. Sharabi O, et al. Among authors: shifman jm. Protein Eng Des Sel. 2009 Oct;22(10):641-8. doi: 10.1093/protein/gzp045. Epub 2009 Jul 30. Protein Eng Des Sel. 2009. PMID: 19643977 Free PMC article.

7

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

Fromer M, Shifman JM. Fromer M, et al. Among authors: shifman jm. PLoS Comput Biol. 2009 Dec;5(12):e1000627. doi: 10.1371/journal.pcbi.1000627. Epub 2009 Dec 24. PLoS Comput Biol. 2009. PMID: 20041208 Free PMC article.

8

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. Filchtinski D, et al. Among authors: shifman jm. J Mol Biol. 2010 Jun 11;399(3):422-35. doi: 10.1016/j.jmb.2010.03.046. Epub 2010 Mar 31. J Mol Biol. 2010. PMID: 20361980

9

Optimizing energy functions for protein-protein interface design.

Sharabi O, Yanover C, Dekel A, Shifman JM. Sharabi O, et al. Among authors: shifman jm. J Comput Chem. 2011 Jan 15;32(1):23-32. doi: 10.1002/jcc.21594. J Comput Chem. 2011. PMID: 20623647

10

Multispecific recognition: mechanism, evolution, and design.

Erijman A, Aizner Y, Shifman JM. Erijman A, et al. Among authors: shifman jm. Biochemistry. 2011 Feb 8;50(5):602-11. doi: 10.1021/bi101563v. Epub 2011 Jan 13. Biochemistry. 2011. PMID: 21229991 Review.

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