From sequence to function through structure: Deep learning for protein design

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

(2022) Bin Huang et al.   NATURE

Protein sequence design with a learned potential

(2022) Namrata Anand et al.   Nature Communications

Machine learning-aided engineering of hydrolases for PET depolymerization

(2022) Hongyuan Lu et al.   NATURE

ColabFold: making protein folding accessible to all

(2022) Milot Mirdita et al.   NATURE METHODS

DeepLoc 2.0: multi-label subcellular localization prediction using protein language models

(2022) Vineet Thumuluri et al.   NUCLEIC ACIDS RESEARCH

NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning

(2022) Magnus Haraldson Høie et al.   NUCLEIC ACIDS RESEARCH

Computational design of mechanically coupled axle-rotor protein assemblies

(2022) A. Courbet et al.   SCIENCE

Constructing benchmark test sets for biological sequence analysis using independent set algorithms

(2022) Samantha Petti et al.   PLoS Computational Biology

TMbed: transmembrane proteins predicted through language model embeddings

(2022) Michael Bernhofer et al.   BMC BIOINFORMATICS

Cloud labs: where robots do the research

(2022) Carrie Arnold   NATURE

Scaffolding protein functional sites using deep learning

(2022) Jue Wang et al.   SCIENCE

ProtGPT2 is a deep unsupervised language model for protein design

(2022) Noelia Ferruz et al.   Nature Communications

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

(2022) Raphael R. Eguchi et al.   PLoS Computational Biology

The Rise of Molecular Glues

(2021) Stuart L. Schreiber   CELL

Embeddings from deep learning transfer GO annotations beyond homology

(2021) Maria Littmann et al.   Scientific Reports

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

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

(2021) Alexander Rives et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emerging Trends in Cancer Drug Discovery—From Drugging the “Undruggable” to Overcoming Resistance

(2021) Joachim Rudolph et al.   Cancer Discovery

A Brief History of De Novo Protein Design: Minimal, Rational, and Computational

(2021) Derek N. Woolfson   JOURNAL OF MOLECULAR BIOLOGY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

The Surprising Story of Fusicoccin: A Wilt-Inducing Phytotoxin, a Tool in Plant Physiology and a 14-3-3-Targeted Drug

(2021) Mauro Marra et al.   Biomolecules

Protein Design with Deep Learning

(2021) Marianne Defresne et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Learning the local landscape of protein structures with convolutional neural networks

(2021) Anastasiya V. Kulikova et al.   JOURNAL OF BIOLOGICAL PHYSICS

De novo protein design by deep network hallucination

(2021) Ivan Anishchenko et al.   NATURE

Disease variant prediction with deep generative models of evolutionary data

(2021) Jonathan Frazer et al.   NATURE

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Computed structures of core eukaryotic protein complexes

(2021) Ian R. Humphreys et al.   SCIENCE

The generative capacity of probabilistic protein sequence models

(2021) Francisco McGee et al.   Nature Communications

Protein embeddings and deep learning predict binding residues for various ligand classes

(2021) Maria Littmann et al.   Scientific Reports

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 potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

A watershed moment for protein structure prediction

(2020) Mohammed AlQuraishi   NATURE

Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface

(2020) Uddhav K. Shigdel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and Flexible Protein Design Using Deep Graph Neural Networks

(2020) Alexey Strokach et al.   Cell Systems

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Remote homology search with hidden Potts models

(2020) Grey W. Wilburn et al.   PLoS Computational Biology

FunFam protein families improve residue level molecular function prediction

(2019) Linus Scheibenreif et al.   BMC BIOINFORMATICS

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

An operating system for the biology lab

(2019) Michael Segal   NATURE

Make more digital twins

(2019) Fei Tao et al.   NATURE

Advances in protein structure prediction and design

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

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

(2019) Satria A Kautsar et al.   NUCLEIC ACIDS RESEARCH

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

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

Modeling aspects of the language of life through transfer-learning protein sequences

(2019) Michael Heinzinger et al.   BMC BIOINFORMATICS

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

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

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

Digital Twins: The Convergence of Multimedia Technologies

(2018) Abdulmotaleb El Saddik   IEEE MULTIMEDIA

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN

(2018) Quinlan L. Sievers et al.   SCIENCE

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

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

The Molecular Tweezer CLR01 Stabilizes a Disordered Protein–Protein Interface

(2017) David Bier et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

One-step design of a stable variant of the malaria invasion protein RH5 for use as a vaccine immunogen

(2017) Ivan Campeotto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Algorithms for protein design

(2016) Pablo Gainza et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

SPLINTS: small-molecule protein ligand interface stabilizers

(2016) Eric S Fischer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Natural Products as Sources of New Drugs from 1981 to 2014

(2016) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

The automated lab

(2014) Erika Check Hayden   NATURE

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

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

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry