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 …

The coral microbiome: towards an understanding of the molecular mechanisms of coral–microbiota interactions

AR Mohamed, MA Ochsenkühn… - FEMS Microbiology …, 2023‏ - academic.oup.com
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms,
some of which are implicated in vital functions, such as those related to resilience against …

AlphaFold2 structures guide prospective ligand discovery

J Lyu, N Kapolka, R Gumpper, A Alon, L Wang… - Science, 2024‏ - science.org
AlphaFold2 (AF2) models have had wide impact but mixed success in retrospective ligand
recognition. We prospectively docked large libraries against unrefined AF2 models of the σ2 …

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 …

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function

F Boadu, H Cao, J Cheng - Bioinformatics, 2023‏ - academic.oup.com
Motivation Millions of protein sequences have been generated by numerous genome and
transcriptome sequencing projects. However, experimentally determining the function of the …

Advances and challenges in biotechnological production of chondroitin sulfate and its oligosaccharides

W Zhang, R Xu, J Chen, H **ong, Y Wang… - International journal of …, 2023‏ - Elsevier
Chondroitin sulfate (CS) is a member of glycosaminoglycans (GAGs) and has critical
physiological functions. CS is widely applied in medical and clinical fields. Currently, the …

Extremozymes: Challenges and Opportunities on the Road to Novel Enzymes Production.

DIJ Salas-Bruggink, J Sánchez-San Martín, G Leiva… - Process …, 2024‏ - Elsevier
Extremozymes, enzymes derived from extremophilic organisms, have gained significant
attention in industrial applications due to their remarkable resistance to extreme conditions …

Advancing structural biology through breakthroughs in AI

L Aithani, E Alcaide, S Bartunov, CDO Cooper… - Current Opinion in …, 2023‏ - Elsevier
The past century has witnessed an exponential increase in our atomic-level understanding
of molecular and cellular mechanisms from a structural perspective, with multiple landmark …

[HTML][HTML] Cell phenotypes can be predicted from propensities of protein conformations

R Nussinov, Y Liu, W Zhang, H Jang - Current opinion in structural biology, 2023‏ - Elsevier
Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities
of the conformations can be predictors of cell function. The conformational states that the …

FuncPhos-STR: An integrated deep neural network for functional phosphosite prediction based on AlphaFold protein structure and dynamics

G Zhang, C Zhang, M Cai, C Luo, F Zhu… - International Journal of …, 2024‏ - Elsevier
Phosphorylation modifications play important regulatory roles in most biological processes.
However, the functional assignment for the vast majority of the identified phosphosites …