Toward complete rational control over protein structure and function through computational design

Publisher Correction: Modular and tunable biological feedback control using a de novo protein switch

(2020) Andrew H. Ng et al.   NATURE

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures

(2020) Jianfu Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mathematical Models of Protease-Based Enzymatic Biosensors

(2020) Deepak K. Agrawal et al.   ACS Synthetic Biology

Intrinsic Disorder-Based Design of Stable Globular Proteins

(2020) Galina S. Nagibina et al.   Biomolecules

Macromolecular modeling and design in Rosetta: recent methods and frameworks

(2020) Julia Koehler Leman et al.   NATURE METHODS

De novo protein design enables the precise induction of RSV-neutralizing antibodies

(2020) Fabian Sesterhenn et al.   SCIENCE

Packing of apolar side chains enables accurate design of highly stable membrane proteins

(2019) Marco Mravic et al.   SCIENCE

Five computational developability guidelines for therapeutic antibody profiling

(2019) Matthew I. J. Raybould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catching a SPY: Using the SpyCatcher-SpyTag and Related Systems for Labeling and Localizing Bacterial Proteins

(2019) Daniel Hatlem et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Engineering proteins for allosteric control by light or ligands

(2019) Onur Dagliyan et al.   Nature Protocols

A novel epitope-presenting thermostable scaffold for the development of highly specific IGF-1/-2 antibodies

(2019) Carmen Peeß et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

De novo design of bioactive protein switches

(2019) Robert A. Langan et al.   NATURE

Integration of the Rosetta Suite with the Python Software Stack via reproducible packaging and core programming interfaces for distributed simulation

(2019) Alexander S. Ford et al.   PROTEIN SCIENCE

Identifying protein-protein interface via a novel multi-scale local sequence and structural representation

(2019) Fei Guo et al.   BMC BIOINFORMATICS

A Computational Protocol for Regulating Protein Binding Reactions with a Light-Sensitive Protein Dimer

(2019) Frank D. Teets et al.   JOURNAL OF MOLECULAR BIOLOGY

Discovery and engineering of enhanced SUMO protease enzymes

(2018) Yue-Ting K. Lau et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program

(2018) Sharon L. Guffy et al.   Journal of Chemical Information and Modeling

Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design

(2018) Jack B. Maguire et al.   Journal of Chemical Theory and Computation

De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles

(2018) Shao-Qing Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability

(2018) Adi Goldenzweig et al.   MOLECULAR CELL

Light-activated protein interaction with high spatial subcellular confinement

(2018) Lorena Benedetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate computational design of multipass transmembrane proteins

(2018) Peilong Lu et al.   SCIENCE

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides

(2018) Garry W. Buchko et al.   PROTEIN SCIENCE

Computational analysis of the amino acid interactions that promote or decrease protein solubility

(2018) Qingzhen Hou et al.   Scientific Reports

Programmable design of orthogonal protein heterodimers

(2018) Zibo Chen et al.   NATURE

Simple yet functional phosphate-loop proteins

(2018) Maria Luisa Romero Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rosetta FunFolDes – A general framework for the computational design of functional proteins

(2018) Jaume Bonet et al.   PLoS Computational Biology

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

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

Massively parallel de novo protein design for targeted therapeutics

(2017) Aaron Chevalier et al.   NATURE

Accurate de novo design of hyperstable constrained peptides

(2016) Gaurav Bhardwaj et al.   NATURE

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity

(2016) S. E. Boyken et al.   SCIENCE

Design of structurally distinct proteins using strategies inspired by evolution

(2016) T. M. Jacobs et al.   SCIENCE

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Iterative approach to computational enzyme design

(2012) H. K. Privett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probing Designability via a Generalized Model of Helical Bundle Geometry

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