Deep learning techniques have significantly impacted protein structure prediction and protein design

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

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

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

(2020) Kathy Y. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo design of protein logic gates

(2020) Zibo Chen et al.   SCIENCE

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

(2020) Fabian Sesterhenn et al.   SCIENCE

De novo design of protein peptides to block association of the SARS-CoV-2 spike protein with human ACE2

(2020) Xiaoqiang Huang et al.   Aging-US

A defined structural unit enables de novo design of small-molecule–binding proteins

(2020) Nicholas F. Polizzi et al.   SCIENCE

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

(2020) Longxing Cao et al.   SCIENCE

‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures

(2020) Ewen Callaway   NATURE

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

(2019) Daniel-Adriano Silva et al.   NATURE

Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen

(2019) Fabian Sesterhenn et al.   PLOS BIOLOGY

EvoDesign: Designing Protein–Protein Binding Interactions Using Evolutionary Interface Profiles in Conjunction with an Optimized Physical Energy Function

(2019) Robin Pearce et al.   JOURNAL OF MOLECULAR BIOLOGY

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks

(2019) Yang Li et al.   BIOINFORMATICS

LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins

(2019) Wei Zheng et al.   NUCLEIC ACIDS RESEARCH

Deep‐learning contact‐map guided protein structure prediction in CASP13

(2019) Wei Zheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Distance-based protein folding powered by deep learning

(2019) Jinbo Xu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EvoEF2: accurate and fast energy function for computational protein design

(2019) Xiaoqiang Huang et al.   BIOINFORMATICS

DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins

(2019) Chengxin Zhang et al.   BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP)—Round XIII

(2019) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Design of metalloproteins and novel protein folds using variational autoencoders

(2018) Joe G. Greener et al.   Scientific Reports

Programmable design of orthogonal protein heterodimers

(2018) Zibo Chen 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

Massively parallel de novo protein design for targeted therapeutics

(2017) Aaron Chevalier et al.   NATURE

Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12

(2017) Chengxin Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure prediction using Rosetta in CASP12

(2017) Sergey Ovchinnikov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

Deep learning

(2015) Yann LeCun et al.   NATURE

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

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

Improving accuracy of protein contact prediction using balanced network deconvolution

(2015) Hai-Ping Sun et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Proof of principle for epitope-focused vaccine design

(2014) Bruno E. Correia et al.   NATURE

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

(2014) Carlo Baldassi et al.   PLoS One

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

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Toward optimal fragment generations forab initioprotein structure assembly

(2013) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field

(2012) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

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

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information

(2008) Sitao Wu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS