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 …

Before and after AlphaFold2: An overview of protein structure prediction

LMF Bertoline, AN Lima, JE Krieger… - Frontiers in …, 2023 - frontiersin.org
Three-dimensional protein structure is directly correlated with its function and its
determination is critical to understanding biological processes and addressing human …

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

S Mosalaganti, A Obarska-Kosinska, M Siggel… - Science, 2022 - science.org
INTRODUCTION The eukaryotic nucleus protects the genome and is enclosed by the two
membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear …

Sampling alternative conformational states of transporters and receptors with AlphaFold2

D Del Alamo, D Sala, HS Mchaourab, J Meiler - Elife, 2022 - elifesciences.org
Equilibrium fluctuations and triggered conformational changes often underlie the functional
cycles of membrane proteins. For example, transporters mediate the passage of molecules …

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 …

[HTML][HTML] Revolutionizing medicinal chemistry: the application of artificial intelligence (AI) in early drug discovery

R Han, H Yoon, G Kim, H Lee, Y Lee - Pharmaceuticals, 2023 - mdpi.com
Artificial intelligence (AI) has permeated various sectors, including the pharmaceutical
industry and research, where it has been utilized to efficiently identify new chemical entities …

Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data

W Zheng, Q Wuyun, Y Li, C Zhang, PL Freddolino… - Nature …, 2024 - nature.com
Leveraging iterative alignment search through genomic and metagenome sequence
databases, we report the DeepMSA2 pipeline for uniform protein single-and multichain …

SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2

RA Stein, HS Mchaourab - PLOS Computational Biology, 2022 - journals.plos.org
The unprecedented performance of Deepmind's Alphafold2 in predicting protein structure in
CASP XIV and the creation of a database of structures for multiple proteomes and protein …

When will RNA get its AlphaFold moment?

B Schneider, BA Sweeney, A Bateman… - Nucleic Acids …, 2023 - academic.oup.com
The protein structure prediction problem has been solved for many types of proteins by
AlphaFold. Recently, there has been considerable excitement to build off the success of …

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

K Stahl, A Graziadei, T Dau, O Brock… - Nature …, 2023 - nature.com
While AlphaFold2 can predict accurate protein structures from the primary sequence,
challenges remain for proteins that undergo conformational changes or for which few …