Modeling conformational states of proteins with AlphaFold

Targeting in silico GPCR conformations with ultra-large library screening for hit discovery

(2023) D. Sala et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

(2023) Yuqi Zhang et al.   Journal of Chemical Information and Modeling

AlphaFold2-RAVE: From Sequence to Boltzmann Ranking

(2023) Bodhi P. Vani et al.   Journal of Chemical Theory and Computation

Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning

(2023) Kolja Stahl et al.   NATURE BIOTECHNOLOGY

Evolutionary-scale prediction of atomic-level protein structure with a language model

(2023) Zeming Lin et al.   SCIENCE

Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties

(2023) Davide Sala et al.   Frontiers in Molecular Biosciences

Can AlphaFold2 predict the impact of missense mutations on structure?

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

Impact of protein conformational diversity on AlphaFold predictions

(2022) Tadeo Saldaño et al.   BIOINFORMATICS

AlphaFold2: A Role for Disordered Protein/Region Prediction?

(2022) Carter J. Wilson et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ColabFold: making protein folding accessible to all

(2022) Milot Mirdita et al.   NATURE METHODS

Multi‐state modeling of G‐protein coupled receptors at experimental accuracy

(2022) Lim Heo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sampling alternative conformational states of transporters and receptors with AlphaFold2

(2022) Diego del Alamo et al.   eLife

AlphaFold, Artificial Intelligence (AI), and Allostery

(2022) Ruth Nussinov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter

(2022) Diego del Alamo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling of protein conformational changes with Rosetta guided by limited experimental data

(2022) Davide Sala et al.   STRUCTURE

Structural dynamics: review of time-resolved cryo-EM

(2022) Märt-Erik Mäeots et al.   Acta Crystallographica Section D-Structural Biology

Single-sequence protein structure prediction using a language model and deep learning

(2022) Ratul Chowdhury et al.   NATURE BIOTECHNOLOGY

SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2

(2022) Richard A. Stein et al.   PLoS Computational Biology

Protein structure prediction in the deep learning era

(2022) Zhenling Peng et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources

(2022) Gáspár Pándy-Szekeres et al.   NUCLEIC ACIDS RESEARCH

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

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

Frozen in time: analyzing molecular dynamics with time-resolved cryo-EM

(2022) Sascha Josef Amann et al.   STRUCTURE

Subsecond Time-Resolved Mass Spectrometry in Dynamic Structural Biology

(2021) Cristina Lento et al.   CHEMICAL REVIEWS

AlphaFold and Implications for Intrinsically Disordered Proteins

(2021) Kiersten M. Ruff et al.   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

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

Applying and improving AlphaFold at CASP14

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

The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution

(2020) Paul Campitelli et al.   Annual Review of Biophysics

Machine Learning for Molecular Simulation

(2020) Frank Noé et al.   Annual Review of Physical Chemistry

Machine learning approaches for analyzing and enhancing molecular dynamics simulations

(2020) Yihang Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Use of single-molecule time-series data for refining conformational dynamics in molecular simulations

(2020) Yasuhiro Matsunaga et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Macromolecular modeling and design in Rosetta: recent methods and frameworks

(2020) Julia Koehler Leman et al.   NATURE METHODS

Computational methods for exploring protein conformations

(2020) Jane R. Allison   BIOCHEMICAL SOCIETY TRANSACTIONS

A review of advancements in coarse-grained molecular dynamics simulations

(2020) Soumil Y. Joshi et al.   MOLECULAR SIMULATION

KLIFS: an overhaul after the first 5 years of supporting kinase research

(2020) Georgi K Kanev et al.   NUCLEIC ACIDS RESEARCH

GPCRdb in 2021: integrating GPCR sequence, structure and function

(2020) Albert J Kooistra et al.   NUCLEIC ACIDS RESEARCH

Challenges and opportunities in cryo-EM single-particle analysis

(2019) Dmitry Lyumkis   JOURNAL OF BIOLOGICAL CHEMISTRY

Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources

(2019) Marius Schmidt   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Quo Vadis Biomolecular NMR Spectroscopy?

(2019) Philipp Selenko   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques

(2019) Linda Cerofolini et al.   Biomolecules

An atomistic view of the YiiP structural changes upon zinc(II) binding

(2019) Davide Sala et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

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

(2019) Chengxin Zhang et al.   BIOINFORMATICS

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS