How accurately can one predict drug binding modes using AlphaFold models?

M Karelina, JJ Noh, RO Dror - Elife, 2023 - elifesciences.org
Computational prediction of protein structure has been pursued intensely for decades,
motivated largely by the goal of using structural models for drug discovery. Recently …

AI-based protein structure prediction in drug discovery: impacts and challenges

M Schauperl, RA Denny - Journal of Chemical Information and …, 2022 - ACS Publications
Proteins are the molecular machinery of the human body, and their malfunctioning is often
responsible for diseases, making them crucial targets for drug discovery. The three …

AlphaFold2 protein structure prediction: Implications for drug discovery

N Borkakoti, JM Thornton - Current opinion in structural biology, 2023 - Elsevier
The drug discovery process involves designing compounds to selectively interact with their
targets. The majority of therapeutic targets for low molecular weight (small molecule) drugs …

[PDF][PDF] 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 …

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 predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

TC Terwilliger, D Liebschner, TI Croll, CJ Williams… - Nature …, 2024 - nature.com
Artificial intelligence-based protein structure prediction methods such as AlphaFold have
revolutionized structural biology. The accuracies of these predictions vary, however, and …

A structural biology community assessment of AlphaFold2 applications

M Akdel, DEV Pires, EP Pardo, J Jänes… - Nature Structural & …, 2022 - nature.com
Most proteins fold into 3D structures that determine how they function and orchestrate the
biological processes of the cell. Recent developments in computational methods for protein …

Modelling three-dimensional protein structures for applications in drug design

T Schmidt, A Bergner, T Schwede - Drug discovery today, 2014 - Elsevier
Highlights•The majority of proteins encoded in a genome are accessible by structure
modelling.•Modelling can provide accurate target predictions for structure-based drug …

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

D Sala, PW Hildebrand, J Meiler - Frontiers in Molecular Biosciences, 2023 - frontiersin.org
Determining the three-dimensional structure of proteins in their native functional states has
been a longstanding challenge in structural biology. While integrative structural biology has …

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 …