A backbone-centred energy function of neural networks for protein design

De novo sequence redesign of a functional Ras‐binding domain globally inverted the surface charge distribution and led to extreme thermostability

(2021) Ruicun Liu et al.   BIOTECHNOLOGY AND BIOENGINEERING

Expanding the space of protein geometries by computational design of de novo fold families

(2020) Xingjie Pan et al.   SCIENCE

How directed evolution reshapes the energy landscape in an enzyme to boost catalysis

(2020) Renee Otten et al.   SCIENCE

The role of local versus nonlocal physicochemical restraints in determining protein native structure

(2020) Jeffrey Skolnick et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

What has de novo protein design taught us about protein folding and biophysics?

(2019) David Baker   PROTEIN SCIENCE

Increasing the efficiency and accuracy of the ABACUS protein sequence design method

(2019) Peng Xiong et al.   BIOINFORMATICS

Computational design of a modular protein sense-response system

(2019) Anum A. Glasgow et al.   SCIENCE

Accurate computational design of multipass transmembrane proteins

(2018) Peilong Lu et al.   SCIENCE

De novo design of a fluorescence-activating β-barrel

(2018) Jiayi Dou et al.   NATURE

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

Principles for designing proteins with cavities formed by curved β sheets

(2017) Enrique Marcos et al.   SCIENCE

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension

(2016) James T. MacDonald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design of structurally distinct proteins using strategies inspired by evolution

(2016) T. M. Jacobs et al.   SCIENCE

Exploring the repeat protein universe through computational protein design

(2015) TJ Brunette et al.   NATURE

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

(2015) Predrag Kukic et al.   PLoS Computational Biology

Computational design of water-soluble α-helical barrels

(2014) Andrew R. Thomson et al.   SCIENCE

Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability

(2014) Peng Xiong et al.   Nature Communications

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Probing Designability via a Generalized Model of Helical Bundle Geometry

(2010) Gevorg Grigoryan et al.   JOURNAL OF MOLECULAR BIOLOGY

An exciting but challenging road ahead for computational enzyme design

(2010) David Baker   PROTEIN SCIENCE

De novo backbone scaffolds for protein design

(2009) James T. MacDonald et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE