Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes

(2023) Shoshana J. Wodak et al.   Annual Review of Biophysics

AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor

(2023) Feng Ren et al.   Chemical Science

Prediction of protein assemblies by structure sampling followed by interface‐focused scoring

(2023) Kliment Olechnovič et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

(2023) Hugo Schweke et al.   PROTEOMICS

Protein structure predictions to atomic accuracy with AlphaFold

(2022) John Jumper et al.   NATURE METHODS

ColabFold: making protein folding accessible to all

(2022) Milot Mirdita et al.   NATURE METHODS

ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction

(2022) Jérôme Tubiana et al.   NATURE METHODS

Improved prediction of protein-protein interactions using AlphaFold2

(2022) Patrick Bryant et al.   Nature Communications

A structural biology community assessment of AlphaFold2 applications

(2022) Mehmet Akdel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

State-of-the-Art Estimation of Protein Model Accuracy Using AlphaFold

(2022) James P. Roney et al.   PHYSICAL REVIEW LETTERS

The impact of AlphaFold Protein Structure Database on the fields of life sciences

(2022) Mihaly Varadi et al.   PROTEOMICS

Novel machine learning approaches revolutionize protein knowledge

(2022) Nicola Bordin et al.   TRENDS IN BIOCHEMICAL SCIENCES

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants

(2021) Johnathan D. Guest et al.   STRUCTURE

Extending the New Generation of Structure Predictors to Account for Dynamics and Allostery

(2021) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

(2021) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2021) Minkyung Baek et al.   SCIENCE

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

Applying and improving AlphaFold at CASP14

(2021) John Jumper et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Nanobodies to study protein conformational states

(2020) Tomasz Uchański et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Application of docking methodologies to modeled proteins

(2020) Amar Singh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2020) Ewen Callaway   NATURE

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space

(2019) Matteo T. Degiacomi   STRUCTURE

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

(2019) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Machine learning for protein folding and dynamics

(2019) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition

(2019) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The challenge of modeling protein assemblies: the CASP12-CAPRI experiment

(2017) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of protein assembly prediction in CASP12

(2017) Aleix Lafita 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

DockQ: A Quality Measure for Protein-Protein Docking Models

(2016) Sankar Basu et al.   PLoS One

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta

(2016) Sergey Ovchinnikov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational prediction of protein interfaces: A review of data driven methods

(2015) Li C. Xue et al.   FEBS LETTERS

Structural templates for comparative protein docking

(2015) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How cryo-EM is revolutionizing structural biology

(2015) Xiao-chen Bai et al.   TRENDS IN BIOCHEMICAL SCIENCES

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

Blind prediction of interfacial water positions in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

(2013) Rocco Moretti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Intertwined Associations in Structures of Homooligomeric Proteins

(2013) Stephen S. MacKinnon et al.   STRUCTURE

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

Conformational stability and folding mechanisms of dimeric proteins

(2008) Jessica A.O. Rumfeldt et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY