Computational approaches streamlining drug discovery

AV Sadybekov, V Katritch - Nature, 2023 - nature.com
Computer-aided drug discovery has been around for decades, although the past few years
have seen a tectonic shift towards embracing computational technologies in both academia …

Modeling conformational states of proteins with AlphaFold

D Sala, F Engelberger, HS Mchaourab… - Current Opinion in …, 2023 - Elsevier
Many proteins exert their function by switching among different structures. Knowing the
conformational ensembles affiliated with these states is critical to elucidate key mechanistic …

AlphaFold2 and its applications in the fields of biology and medicine

Z Yang, X Zeng, Y Zhao, R Chen - Signal Transduction and Targeted …, 2023 - nature.com
Abstract AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind
that can predict three-dimensional (3D) structures of proteins from amino acid sequences …

How good are AlphaFold models for docking-based virtual screening?

V Scardino, JI Di Filippo, CN Cavasotto - Iscience, 2023 - cell.com
A crucial component in structure-based drug discovery is the availability of high-quality three-
dimensional structures of the protein target. Whenever experimental structures were not …

[HTML][HTML] Integrating structure-based approaches in generative molecular design

M Thomas, A Bender, C de Graaf - Current Opinion in Structural Biology, 2023 - Elsevier
Generative molecular design for drug discovery and development has seen a recent
resurgence promising to improve the efficiency of the design-make-test-analyse cycle; by …

Evaluation of AlphaFold2 structures as docking targets

M Holcomb, YT Chang, DS Goodsell, S Forli - Protein Science, 2023 - Wiley Online Library
AlphaFold2 is a promising new tool for researchers to predict protein structures and
generate high‐quality models, with low backbone and global root‐mean‐square deviation …

AlphaFold, allosteric, and orthosteric drug discovery: Ways forward

R Nussinov, M Zhang, Y Liu, H Jang - Drug discovery today, 2023 - Elsevier
Highlights•AlphaFold models have rigid protein structures.•Advanced deep algorithms fed
relevant data can accurately predict structures.•Algorithmic advances can harness …

Are deep learning structural models sufficiently accurate for virtual screening? application of docking algorithms to AlphaFold2 predicted structures

AM Díaz-Rovira, H Martín, T Beuming… - Journal of Chemical …, 2023 - ACS Publications
Machine learning-based protein structure prediction algorithms, such as RosettaFold and
AlphaFold2, have greatly impacted the structural biology field, arousing a fair amount of …

State-specific protein–ligand complex structure prediction with a multiscale deep generative model

Z Qiao, W Nie, A Vahdat, TF Miller III… - Nature Machine …, 2024 - nature.com
The binding complexes formed by proteins and small molecule ligands are ubiquitous and
critical to life. Despite recent advancements in protein structure prediction, existing …

Are deep learning structural models sufficiently accurate for free-energy calculations? Application of FEP+ to AlphaFold2-predicted structures

T Beuming, H Martín, AM Díaz-Rovira… - Journal of Chemical …, 2022 - ACS Publications
The availability of AlphaFold2 has led to great excitement in the scientific community─
particularly among drug hunters─ due to the ability of the algorithm to predict protein …