Revolutionizing peptide‐based drug discovery: Advances in the post‐AlphaFold era

L Chang, A Mondal, B Singh… - Wiley …, 2024 - Wiley Online Library
Peptide‐based drugs offer high specificity, potency, and selectivity. However, their inherent
flexibility and differences in conformational preferences between their free and bound states …

[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 …

[HTML][HTML] Highly accurate protein structure prediction for the human proteome

K Tunyasuvunakool, J Adler, Z Wu, T Green, M Zielinski… - Nature, 2021 - nature.com
Protein structures can provide invaluable information, both for reasoning about biological
processes and for enabling interventions such as structure-based drug development or …

Molecular dynamics in the endgame of protein structure prediction

MR Lee, J Tsai, D Baker, PA Kollman - Journal of molecular biology, 2001 - Elsevier
In order adequately to sample conformational space, methods for protein structure prediction
make necessary simplifications that also prevent them from being as accurate as desired …

[HTML][HTML] New avenues in artificial-intelligence-assisted drug discovery

C Cerchia, A Lavecchia - Drug Discovery Today, 2023 - Elsevier
Over the past decade, the amount of biomedical data available has grown at unprecedented
rates. Increased automation technology and larger data volumes have encouraged the use …

[HTML][HTML] The case for post-predictional modifications in the AlphaFold Protein Structure Database

H Bagdonas, CA Fogarty, E Fadda… - Nature structural & …, 2021 - nature.com
To the editor—AlphaFold2 has arrived to change workflows in structural biology, for good.
However, the algorithm does not account for essential modifications that affect protein …

Homology modeling in drug discovery: current trends and applications

CN Cavasotto, SS Phatak - Drug discovery today, 2009 - Elsevier
As structural genomics (SG) projects continue to deposit representative 3D structures of
proteins, homology modeling methods will play an increasing role in structure-based drug …

[HTML][HTML] ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid …

JL Klepeis, CA Floudas - Biophysical journal, 2003 - cell.com
The field of computational biology has been revolutionized by recent advances in genomics.
The completion of a number of genome projects, including that of the human genome, has …

[HTML][HTML] 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 …

Coevolutionary signals across protein lineages help capture multiple protein conformations

F Morcos, B Jana, T Hwa… - Proceedings of the …, 2013 - National Acad Sciences
A long-standing problem in molecular biology is the determination of a complete functional
conformational landscape of proteins. This includes not only proteins' native structures, but …