A structural biology community assessment of AlphaFold2 applications

Can AlphaFold2 predict the impact of missense mutations on structure?

(2022) Gwen R. Buel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Predicting and interpreting large-scale mutagenesis data using analyses of protein stability and conservation

(2022) Magnus Haraldson Høie et al.   Cell Reports

ColabFold: making protein folding accessible to all

(2022) Milot Mirdita et al.   NATURE METHODS

Improved prediction of protein-protein interactions using AlphaFold2

(2022) Patrick Bryant et al.   Nature Communications

SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability

(2021) Gen Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

eIF2B conformation and assembly state regulates the integrated stress response

(2021) Michael Schoof et al.   eLife

Critical assessment of protein intrinsic disorder prediction

(2021) Marco Necci et al.   NATURE METHODS

Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding

(2021) Michael Taschner et al.   EMBO JOURNAL

Exploring amino acid functions in a deep mutational landscape

(2021) Alistair S Dunham et al.   Molecular Systems Biology

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

Limits and potential of combined folding and docking

(2021) Gabriele Pozzati et al.   BIOINFORMATICS

Machine learning in protein structure prediction

(2021) Mohammed AlQuraishi   CURRENT OPINION IN CHEMICAL BIOLOGY

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

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

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

ThermoMutDB: a thermodynamic database for missense mutations

(2020) Joicymara S Xavier et al.   NUCLEIC ACIDS RESEARCH

DynaMut2 : Assessing changes in stability and flexibility upon single and multiple point missense mutations

(2020) Carlos H.M. Rodrigues et al.   PROTEIN SCIENCE

Predicting binding sites from unbound versus bound protein structures

(2020) Jordan J. Clark et al.   Scientific Reports

Geometricus represents protein structures as shape-mers derived from moment invariants

(2020) Janani Durairaj et al.   BIOINFORMATICS

ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B

(2020) Alisa F. Zyryanova et al.   MOLECULAR CELL

ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years

(2020) Rahul Nikam et al.   NUCLEIC ACIDS RESEARCH

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

(2020) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

Elucidating the druggability of the human proteome with eFindSite

(2019) Omar Kana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

DEGS1-associated aberrant sphingolipid metabolism impairs nervous system function in humans

(2019) Gergely Karsai et al.   JOURNAL OF CLINICAL INVESTIGATION

FoldX 5.0: Working with RNA, small molecules and a new graphical interface

(2019) Javier Delgado et al.   BIOINFORMATICS

eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response

(2019) Lillian R. Kenner et al.   SCIENCE

End-to-End Differentiable Learning of Protein Structure

(2019) Mohammed AlQuraishi   Cell Systems

Distance-based protein folding powered by deep learning

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

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

(2018) Carlos HM Rodrigues et al.   NUCLEIC ACIDS RESEARCH

An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure

(2018) Raghu Bhagavat et al.   STRUCTURE

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model

(2018) Ivan Anishchenko et al.   BIOPHYSICAL JOURNAL

Protein Data Bank: the single global archive for 3D macromolecular structure data

(2018) et al.   NUCLEIC ACIDS RESEARCH

Dockground: A comprehensive data resource for modeling of protein complexes

(2017) Petras J. Kundrotas et al.   PROTEIN SCIENCE

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

(2017) Sheng Wang et al.   PLoS Computational Biology

AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms

(2016) Pradeep Anand Ravindranath et al.   BIOINFORMATICS

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

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

ProViz—a web-based visualization tool to investigate the functional and evolutionary features of protein sequences

(2016) Peter Jehl et al.   NUCLEIC ACIDS RESEARCH

The SWISS-MODEL Repository—new features and functionality

(2016) Stefan Bienert et al.   NUCLEIC ACIDS RESEARCH

DockQ: A Quality Measure for Protein-Protein Docking Models

(2016) Sankar Basu et al.   PLoS One

MAESTRO - multi agent stability prediction upon point mutations

(2015) Josef Laimer et al.   BMC BIOINFORMATICS

Crystal structure of human stearoyl–coenzyme A desaturase in complex with substrate

(2015) Hui Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability

(2015) Vincent Frappier et al.   NUCLEIC ACIDS RESEARCH

Crystal structure of human stearoyl–coenzyme A desaturase in complex with substrate

(2015) Hui Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

(2014) D. E. V. Pires et al.   NUCLEIC ACIDS RESEARCH

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

ggplot2: Elegant Graphics for Data Analysis by WICKHAM, H.

(2011) Leland Wilkinson   BIOMETRICS

Metagenomics and the protein universe

(2011) Adam Godzik   CURRENT OPINION IN STRUCTURAL BIOLOGY

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Graphical Models of Residue Coupling in Protein Families

(2008) J. Thomas et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

Using scores derived from statistical coupling analysis to distinguish correct and incorrect folds in de-novo protein structure prediction

(2007) Gail J. Bartlett et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS