Protein sequence design with a learned potential

Protein sequence design by conformational landscape optimization

(2021) Christoffer Norn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Low-N protein engineering with data-efficient deep learning

(2021) Surojit Biswas et al.   NATURE METHODS

The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach

(2021) Sergio Romero-Romero et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein sequence design with deep generative models

(2021) Zachary Wu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

De novo protein design by deep network hallucination

(2021) Ivan Anishchenko et al.   NATURE

DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet

(2020) Yifei Qi et al.   Journal of Chemical Information and Modeling

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of Novel Gain-of-Function Mutations Guided by Structure-Based Deep Learning

(2020) Raghav Shroff et al.   ACS Synthetic Biology

Fast and Flexible Protein Design Using Deep Graph Neural Networks

(2020) Alexey Strokach et al.   Cell Systems

Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion

(2020) Shane J. Caldwell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo design of potent and selective mimics of IL-2 and IL-15

(2019) Daniel-Adriano Silva et al.   NATURE

The PSIPRED Protein Analysis Workbench: 20 years on

(2019) Daniel W A Buchan et al.   NUCLEIC ACIDS RESEARCH

Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)

(2019) Andrew W. Senior et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational design of a modular protein sense-response system

(2019) Anum A. Glasgow et al.   SCIENCE

To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map

(2019) Sheng Chen et al.   Journal of Chemical Information and Modeling

ProDCoNN: Protein design using a convolutional neural network

(2019) Yuan Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design

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

SPIN2: Predicting sequence profiles from protein structures using deep neural networks

(2018) James O'Connell et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Gene3D: Extensive prediction of globular domains in proteins

(2017) Tony E Lewis et al.   NUCLEIC ACIDS RESEARCH

Computational design of environmental sensors for the potent opioid fentanyl

(2017) Matthew J Bick et al.   eLife

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

CATH: an expanded resource to predict protein function through structure and sequence

(2016) Natalie L. Dawson et al.   NUCLEIC ACIDS RESEARCH

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

(2016) S. E. Boyken et al.   SCIENCE

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy

(2015) Po-Ssu Huang et al.   Nature Chemical Biology

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Proof of principle for epitope-focused vaccine design

(2014) Bruno E. Correia et al.   NATURE

Computational design of a self-assembling symmetrical β-propeller protein

(2014) Arnout R. D. Voet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment-based local and energy-based nonlocal profiles

(2014) Zhixiu Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

De novo design of a transmembrane Zn2+-transporting four-helix bundle

(2014) Nathan H. Joh et al.   SCIENCE

Computational design of ligand-binding proteins with high affinity and selectivity

(2013) Christine E. Tinberg et al.   NATURE

A Pareto-Optimal Refinement Method for Protein Design Scaffolds

(2013) Lucas Gregorio Nivón et al.   PLoS One

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

REFMAC5 for the refinement of macromolecular crystal structures

(2011) Garib N. Murshudov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

Algorithm discovery by protein folding game players

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

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces

(2011) G. Grigoryan et al.   SCIENCE

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY

A series of PDB related databases for everyday needs

(2010) R. P. Joosten et al.   NUCLEIC ACIDS RESEARCH

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

(2010) J. B. Siegel et al.   SCIENCE

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE