ProtGPT2 is a deep unsupervised language model for protein design

ProteinBERT: a universal deep-learning model of protein sequence and function

(2022) Nadav Brandes et al.   BIOINFORMATICS

Dreaming ideal protein structures

(2022) Noelia Ferruz et al.   NATURE BIOTECHNOLOGY

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

Protlego: A Python package for the analysis and design of chimeric proteins

(2021) Noelia Ferruz et al.   BIOINFORMATICS

Extension of a de novo TIM barrel with a rationally designed secondary structure element

(2021) Jonas Gregor Wiese et al.   PROTEIN SCIENCE

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation

(2021) Gábor Erdős et al.   NUCLEIC ACIDS RESEARCH

Learning the protein language: Evolution, structure, and function

(2021) Tristan Bepler et al.   Cell Systems

Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks

(2021) Noelia Ferruz et al.   Frontiers in Molecular Biosciences

DeepIDP-2L: protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network

(2021) Yi-Jun Tang et al.   BIOINFORMATICS

BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models

(2021) Hong-Liang Li et al.   NUCLEIC ACIDS RESEARCH

A newly introduced salt bridge cluster improves structural and biophysical properties of de novo TIM barrels

(2021) Sina Kordes et al.   PROTEIN SCIENCE

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Multi-state design of flexible proteins predicts sequences optimal for conformational change

(2020) Marion F. Sauer et al.   PLoS Computational Biology

Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design

(2020) Noelia Ferruz et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational design of transmembrane pores

(2020) Chunfu Xu et al.   NATURE

CATH: increased structural coverage of functional space

(2020) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

The PSIPRED Protein Analysis Workbench: 20 years on

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

Machine-learning-guided directed evolution for protein engineering

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

BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Unified rational protein engineering with sequence-based deep representation learning

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

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

(2019) Chuan Tian et al.   Journal of Chemical Theory and Computation

De novo design of a non-local β-sheet protein with high stability and accuracy

(2018) Enrique Marcos et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

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

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

(2016) S. Doerr et al.   Journal of Chemical Theory and Computation

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

Insights from Fragment Hit Binding Assays by Molecular Simulations

(2015) Noelia Ferruz et al.   Journal of Chemical Information and Modeling

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

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

Unexpected features of the dark proteome

(2015) Nelson Perdigão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global view of the protein universe

(2014) S. Nepomnyachiy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ECOD: An Evolutionary Classification of Protein Domains

(2014) Hua Cheng et al.   PLoS Computational Biology

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Maps of protein structure space reveal a fundamental relationship between protein structure and function

(2011) M. Osadchy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation