Julia M. Shifman

发表

Optimizing energy functions for protein–protein interface design

Chen Yanover, Oz Sharabi, Ayelet Dekel, 2011, J. Comput. Chem..

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins

Menachem Fromer, Julia M. Shifman, M. Fromer, 2009, PLoS Comput. Biol..

Dead‐end elimination for multistate protein design

Menachem Fromer, Chen Yanover, Julia M. Shifman, 2007, J. Comput. Chem..

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

Junichi Takagi, Stephen L. Mayo, Timothy A. Springer, 2000, Nature Structural Biology.

How Structure Defines Affinity in Protein-Protein Interactions

Julia M. Shifman, J. Shifman, Ariel Erijman, 2014, PloS one.

Targeting Ras with protein engineering

Julia M. Shifman, J. Shifman, A. Tomazini, 2023, Oncotarget.

Designed loop extension followed by combinatorial screening confers high specificity to a broad matrix metalloproteinaseinhibitor.

Julia M. Shifman, J. Shifman, E. Radisky, 2023, Journal of molecular biology.

A broad matrix metalloproteinase inhibitor with designed loop extension exhibits ultrahigh specificity for MMP-14

Julia M. Shifman, J. Shifman, E. Radisky, 2022, bioRxiv.

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

Julia M. Shifman, J. Shifman, P. Dutton, 1998, Biochemistry.

Climbing Up and Down Binding Landscapes through Deep Mutational Scanning of Three Homologous Protein–Protein Complexes

Julia M. Shifman, Y. Peleg, Michael Heyne, 2021, Journal of the American Chemical Society.

Climbing up and down binding landscapes: a high-throughput study of mutational effects in homologous protein-protein complexes

Julia M. Shifman, Y. Peleg, J. Shifman, 2020, bioRxiv.

Generating quantitative binding landscapes through fractional binding selections combined with deep sequencing and data normalization

Julia M. Shifman, J. Shifman, Michael Heyne, 2020, Nature Communications.

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

Julia M. Shifman, J. Shifman, A. Cohen, 2017, Journal of molecular biology.

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

Philip M. Kim, Julia M. Shifman, J. Shifman, 2019, Journal of molecular biology.

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

Julia M. Shifman, J. Shifman, S. Sidhu, 2016, Proceedings of the National Academy of Sciences.

Allosteric Modu Specificity by A of Protein Cores

Philip M. Kim, Julia M. Shifman, J. Shifman, 2019 .

RASSF effectors couple diverse RAS subfamily GTPases to the Hippo pathway

Julia M. Shifman, J. Shifman, Anamika Singh, 2020, Science Signaling.

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

Julia M. Shifman, J. Shifman, P. Dutton, 2000, Biochemistry.

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

Stefan Mihalas, Stephen L Mayo, Julia M. Shifman, 2006, Proceedings of the National Academy of Sciences.

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

Julia M. Shifman, Y. Peleg, J. Shifman, 2011, Journal of structural biology.

Computational design and experimental optimization of protein binders with prospects for biomedical applications.

Julia M. Shifman, J. Shifman, A. Bonadio, 2021, Protein engineering, design & selection : PEDS.

Modulating calmodulin binding specificity through computational protein design.

Julia M. Shifman, S. L. Mayo, J. Shifman, 2002, Journal of molecular biology.

A KLK4 proteinase substrate capture approach to antagonize PAR1

Julia M. Shifman, J. Shifman, M. Hollenberg, 2021, Scientific Reports.

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

Julia M. Shifman, M. Kosloff, J. Shifman, 2017, Journal of molecular biology.

Protein Engineering by Combined Computational and In Vitro Evolution Approaches.

Julia M. Shifman, J. Shifman, L. Rosenfeld, 2016, Trends in biochemical sciences.

Generating quantitative binding landscapes through fractional binding selections combined with deep sequencing and data normalization

Julia M. Shifman, Michael Heyne, N. Papo, 2020, Nature Communications.

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

Julia M. Shifman, J. Shifman, L. Rosenfeld, 2015, The Journal of Biological Chemistry.

bound calciums /calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two 2+ Ca

Julia M. Shifman, S. L. Mayo, Stefan Mihalas, 2006 .

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

Julia M. Shifman, J. Shifman, N. Papo, 2017, The Journal of Biological Chemistry.

Engineered variants of the Ras effector protein RASSF5 (NORE1A) promote anticancer activities in lung adenocarcinoma

Julia M. Shifman, Y. Peleg, J. Shifman, 2021, The Journal of biological chemistry.

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

Julia M. Shifman, Y. Peleg, Ariel Erijman, 2014, Methods in molecular biology.

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

Oz Sharabi, Julia M. Shifman, Julia M Shifman, 2010, Journal of molecular biology.

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

Julia M. Shifman, Julia M Shifman, Regina Politi, 2009, Journal of molecular biology.

Cold Spots in Protein Binding.

Julia M. Shifman, Jason Shirian, Oz Sharabi, 2016, Trends in biochemical sciences.

Triathlon for energy functions: Who is the winner for design of protein–protein interactions?

Julia M. Shifman, Oz Sharabi, Ayelet Dekel, 2011, Proteins.

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

Julia M. Shifman, S. L. Mayo, J. Shifman, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Computational Design of Protein– Protein Interactions

Julia M. Shifman, J. Shifman, 2009 .

Heme Redox Potential Control in de Novo Designed Four-R-Helix Bundle Proteins †

Julia M. Shifman, J. Shifman, P. Dutton, 2022 .

Multispecific recognition: mechanism, evolution, and design.

Julia M. Shifman, Julia M Shifman, J. Shifman, 2011, Biochemistry.

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

Julia M. Shifman, J. Shifman, N. Papo, 2017, bioRxiv.

Affinity- and Specificity-Enhancing Mutations Are Frequent in Multispecific Interactions between TIMP2 and MMPs

Julia M. Shifman, J. Shifman, Jason Shirian, 2014, PloS one.

Generating quantitative binding landscapes through fractional binding selections, deep sequencing and data normalization

Julia M. Shifman, Michael Heyne, N. Papo, 2019, bioRxiv.

Mapping of the binding landscape for a picomolar protein-protein complex through computation and experiment.

Julia M. Shifman, Jason Shirian, Oz Sharabi, 2014, Structure.

RAS/Effector Interactions from Structural and Biophysical Perspective.

Julia M. Shifman, J. Shifman, Ariel Erijman, 2016, Mini reviews in medicinal chemistry.

Computational methods for controlling binding specificity.

Julia M. Shifman, J. Shifman, Ariel Erijman, 2013, Methods in enzymology.

Intricacies of Beta sheet protein design.

Julia M. Shifman, 2008, Structure.

Computational design of Matrix Metalloprotenaise-9 (MMP-9) resistant to autocleavage

Julia M. Shifman, J. Shifman, O. Kleifeld, 2023, bioRxiv.