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

Journal of structural biology, 2011-08, Vol.175 (2), p.171-177

2011

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

Methods in molecular biology (Clifton, N.J.), 2014-01, Vol.1116, p.89

2014

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

Protein engineering, design and selection, 2021-08, Vol.34

2021

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Targeting Ras with protein engineering

Oncotarget, 2023-07, Vol.14 (1), p.672-687

2023

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

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

2023

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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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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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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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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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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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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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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

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

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

Tradeoff between stability and multispecificity in the design of promiscuous proteins

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

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

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

Targeting Ras with protein engineering

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

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

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

Cold spots are universal in protein–protein interactions

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

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

Optimizing energy functions for protein-protein interface design

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

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

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