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How structure defines affinity in protein-protein interactions

PloS one, 2014-10, Vol.9 (10), p.e110085-e110085

2014

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Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein-protein interfaces

BMC bioinformatics, 2024-04, Vol.25 (1), p.172-172, Article 172

2024

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

Nature communications, 2020-01, Vol.11 (1), p.297-297, Article 297

2020

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

Journal of molecular biology, 2017-11, Vol.429 (22), p.3353-3362

2017

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Tradeoff between stability and multispecificity in the design of promiscuous proteins

PLoS computational biology, 2009-12, Vol.5 (12), p.e1000627

2009

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Ca²⁺/Calmodulin-Dependent Protein Kinase II (CaMKII) Is Activated by Calmodulin with Two Bound Calciums

Proceedings of the National Academy of Sciences - PNAS, 2006-09, Vol.103 (38), p.13968-13973

2006

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Cold Spots in Protein Binding

Trends in biochemical sciences (Amsterdam. Regular ed.), 2016-09, Vol.41 (9), p.739-745

2016

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Exploring the Origins of Binding Specificity through the Computational Redesign of Calmodulin

Proceedings of the National Academy of Sciences - PNAS, 2003-11, Vol.100 (23), p.13274-13279

2003

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

Proceedings of the National Academy of Sciences - PNAS, 2016-08, Vol.113 (31), p.8705-8710

2016

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Protein Engineering by Combined Computational and In Vitro Evolution Approaches

Trends in biochemical sciences (Amsterdam. Regular ed.), 2016-05, Vol.41 (5), p.421-433

2016

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

Journal of the American Chemical Society, 2021-10, Vol.143 (41), p.17261-17275

2021

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

The Journal of biological chemistry, 2021-12, Vol.297 (6), p.101353, Article 101353

2021

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Cold spots are universal in protein–protein interactions

Protein science, 2022-10, Vol.31 (10), p.e4435-n/a

2022

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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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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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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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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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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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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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How structure defines affinity in protein-protein interactions

Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein-protein interfaces

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

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

Tradeoff between stability and multispecificity in the design of promiscuous proteins

Ca²⁺/Calmodulin-Dependent Protein Kinase II (CaMKII) Is Activated by Calmodulin with Two Bound Calciums

Cold Spots in Protein Binding

Exploring the Origins of Binding Specificity through the Computational Redesign of Calmodulin

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

Protein Engineering by Combined Computational and In Vitro Evolution Approaches

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

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

Cold spots are universal in protein–protein interactions

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

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

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

Modulating Calmodulin Binding Specificity through Computational Protein Design

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

Computational Methods for Controlling Binding Specificity

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

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