Linking protein structural and functional change to mutation using amino acid networks

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

(2021) Xianggen Liu et al.   PLoS Computational Biology

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

(2020) Tyler N. Starr et al.   CELL

Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations

(2020) Benjamin J Livesey et al.   Molecular Systems Biology

Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues

(2020) Camila M. Lopes-Ramos et al.   Cell Reports

Establishing a Framework of Using Residue–Residue Interactions in Protein Difference Network Analysis

(2019) Xin-Qiu Yao et al.   Journal of Chemical Information and Modeling

Determining protein structures using deep mutagenesis

(2019) Jörn M. Schmiedel et al.   NATURE GENETICS

Advances in protein structure prediction and design

(2019) Brian Kuhlman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Protein structure-based drug design: from docking to molecular dynamics

(2018) Paweł Śledź et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Application of protoplast technology to CRISPR/Cas9 mutagenesis: from single-cell mutation detection to mutant plant regeneration

(2018) Choun-Sea Lin et al.   PLANT BIOTECHNOLOGY JOURNAL

Rationally Designed Sensing Selectivity and Sensitivity of an Aerolysin Nanopore via Site-Directed Mutagenesis

(2018) Ya-Qian Wang et al.   ACS Sensors

In proteins, the structural responses of a position to mutation rely on the Goldilocks principle: not too many links, not too few

(2018) Rodrigo Dorantes Gilardi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Somatic Gene Editing of GUCY2D by AAV-CRISPR/Cas9 Alters Retinal Structure and Function in Mouse and Macaque

(2018) K. Tyler McCullough et al.   HUMAN GENE THERAPY

Protein Data Bank: the single global archive for 3D macromolecular structure data

(2018) et al.   NUCLEIC ACIDS RESEARCH

T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis

(2018) Yongzhen Xia et al.   NUCLEIC ACIDS RESEARCH

A Single Active Site Mutation in the Pikromycin Thioesterase Generates a More Effective Macrocyclization Catalyst

(2017) Aaron A. Koch et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis of CRISPR–SpyCas9 inhibition by an anti-CRISPR protein

(2017) De Dong et al.   NATURE

The flavivirus capsid protein: Structure, function and perspectives towards drug design

(2017) Edson R.A. Oliveira et al.   VIRUS RESEARCH

NAPS: Network Analysis of Protein Structures

(2016) Broto Chakrabarty et al.   NUCLEIC ACIDS RESEARCH

Protein structural robustness to mutations: an in silico investigation

(2016) Mounia Achoch et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Deep learning

(2015) Yann LeCun et al.   NATURE

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

The construction of an amino acid network for understanding protein structure and function

(2014) Wenying Yan et al.   AMINO ACIDS

Alignment-free protein interaction network comparison

(2014) Waqar Ali et al.   BIOINFORMATICS

The robustness and innovability of protein folds

(2014) Ágnes Tóth-Petróczy et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Measuring the activity of protein variants on a large scale using deep mutational scanning

(2014) Douglas M Fowler et al.   Nature Protocols

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Contact Networks: An Emerging Paradigm in Chemistry

(2012) L. Di Paola et al.   CHEMICAL REVIEWS

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Protein Structural Modularity and Robustness Are Associated with Evolvability

(2011) Mary M. Rorick et al.   Genome Biology and Evolution

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep mutational scanning: assessing protein function on a massive scale

(2011) Carlos L. Araya et al.   TRENDS IN BIOTECHNOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

The sequence–structure relationship and protein function prediction

(2009) M I Sadowski et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Exploring protein fitness landscapes by directed evolution

(2009) Philip A. Romero et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics