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

FEBS letters, 2018-04, Vol.592 (7), p.1122-1134

2018

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

Current opinion in structural biology, 2017-08, Vol.45, p.iv-vi

2017

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Multispecific Recognition: Mechanism, Evolution, and Design

Biochemistry (Easton), 2011-02, Vol.50 (5), p.602-611

2011

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

The Journal of biological chemistry, 2015-10, Vol.290 (43), p.26180-26193

2015

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

Journal of molecular biology, 2017-01, Vol.429 (1), p.97-114

2017

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Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores

Journal of molecular biology, 2019-01, Vol.431 (2), p.336-350

2019

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

Proteins, structure, function, and bioinformatics, 2011-05, Vol.79 (5), p.1487-1498

2011

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What Makes Ras an Efficient Molecular Switch: A Computational, Biophysical, and Structural Study of Ras-GDP Interactions with Mutants of Raf

Journal of molecular biology, 2010-06, Vol.399 (3), p.422-435

2010

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Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding Specificity

Journal of molecular biology, 2009-02, Vol.385 (5), p.1470-1480

2009

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Alteration of the C-Terminal Ligand Specificity of the Erbin PDZ Domain by Allosteric Mutational Effects

Journal of molecular biology, 2014-10, Vol.426 (21), p.3500-3508

2014

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Optimizing energy functions for protein-protein interface design

Journal of computational chemistry, 2011-01, Vol.32 (1), p.23-32

2011

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

Journal of peptide science, 2015-09, Vol.21 (9), p.723-730

2015

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Dead-end elimination for multistate protein design

Journal of computational chemistry, 2007-10, Vol.28 (13), p.2122-2129

2007

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Intricacies of β Sheet Protein Design

Structure (London), 2008-12, Vol.16 (12), p.1751-1752

Shifman, Julia M.

2008

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Modulating Calmodulin Binding Specificity through Computational Protein Design

Journal of molecular biology, 2002-10, Vol.323 (3), p.417-423

2002

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

Biochemistry (Easton), 2000-12, Vol.39 (48), p.14813-14821

2000

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

Nature structural & molecular biology, 2000-08, Vol.7 (8), p.674-678

2000

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Designed Loop Extension Followed by Combinatorial Screening Confers High Specificity to a Broad Matrix Metalloproteinase Inhibitor

Journal of molecular biology, 2023-07, Vol.435 (13), p.168095-168095, Article 168095

2023

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

Protein engineering, design and selection, 2009-10, Vol.22 (10), p.641-648

2009

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Computational Methods for Controlling Binding Specificity

Methods in Enzymology, 2013, Vol.523, p.41-59

2013

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Functionalized de Novo Designed Proteins: Mechanism of Proton Coupling to Oxidation/Reduction in Heme Protein Maquettes

Biochemistry (Easton), 1998-11, Vol.37 (47), p.16815-16827

1998

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Mirror‐Image Random Nonstandard Peptide Integrated Discovery (MI‐RaPID) Technology Yields Highly Stable and Selective Macrocyclic Peptide Inhibitors for Matrix Metallopeptidase 7

Angewandte Chemie, 2024-08

2024

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Development of High Affinity and High Specificity Inhibitors of Matrix Metalloproteinase 14 through Computational Design and Directed EvolutionThis work was supported in part by European Research Council “Ideas Program” ERC-2013-StG by Contract Grant 336041 (to N. P.). The authors declare that they have no conflicts of interest with the contents of this article. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute

The Journal of biological chemistry, 2017-02, Vol.292 (8), p.3481-3495

2017

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Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins: e1000627

PLoS computational biology, 2009-12, Vol.5 (12)

2009

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Synthetic peptides mimicking the binding site of human acetylcholinesterase for its inhibitor fasciculin 2: AChE Mimetic Peptides

Journal of peptide science, 2015-09, Vol.21 (9), p.723-730

2015

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

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

Multispecific Recognition: Mechanism, Evolution, and Design

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

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

Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores

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

What Makes Ras an Efficient Molecular Switch: A Computational, Biophysical, and Structural Study of Ras-GDP Interactions with Mutants of Raf

Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding Specificity

Alteration of the C-Terminal Ligand Specificity of the Erbin PDZ Domain by Allosteric Mutational Effects

Optimizing energy functions for protein-protein interface design

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

Dead-end elimination for multistate protein design

Intricacies of β Sheet Protein Design

Modulating Calmodulin Binding Specificity through Computational Protein Design

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

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

Designed Loop Extension Followed by Combinatorial Screening Confers High Specificity to a Broad Matrix Metalloproteinase Inhibitor

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

Computational Methods for Controlling Binding Specificity

Functionalized de Novo Designed Proteins: Mechanism of Proton Coupling to Oxidation/Reduction in Heme Protein Maquettes

Mirror‐Image Random Nonstandard Peptide Integrated Discovery (MI‐RaPID) Technology Yields Highly Stable and Selective Macrocyclic Peptide Inhibitors for Matrix Metallopeptidase 7

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins: e1000627

Synthetic peptides mimicking the binding site of human acetylcholinesterase for its inhibitor fasciculin 2: AChE Mimetic Peptides

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