Artificial intelligence for drug discovery: Resources, methods, and applications

W Chen, X Liu, S Zhang, S Chen - Molecular Therapy-Nucleic Acids, 2023 - cell.com
Conventional wet laboratory testing, validations, and synthetic procedures are costly and
time-consuming for drug discovery. Advancements in artificial intelligence (AI) techniques …

Surveying over 100 predictors of intrinsic disorder in proteins

B Zhao, L Kurgan - Expert Review of Proteomics, 2021 - Taylor & Francis
Introduction Intrinsic disorder prediction field develops, assesses, and deploys
computational predictors of disorder in protein sequences and constructs and disseminates …

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

A Dhakal, R Gyawali, L Wang, J Cheng - Scientific Data, 2023 - nature.com
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of
biological macromolecular complexes. Picking single-protein particles from cryo-EM …

[HTML][HTML] iTCep: a deep learning framework for identification of T cell epitopes by harnessing fusion features

Y Zhang, X Jian, L Xu, J Zhao, M Lu, Y Lin… - Frontiers in Genetics, 2023 - frontiersin.org
Neoantigens recognized by cytotoxic T cells are effective targets for tumor-specific immune
responses for personalized cancer immunotherapy. Quite a few neoantigen identification …

LMPhosSite: a deep learning-based approach for general protein phosphorylation site prediction using embeddings from the local window sequence and pretrained …

SC Pakhrin, S Pokharel, P Pratyush… - Journal of proteome …, 2023 - ACS Publications
Phosphorylation is one of the most important post-translational modifications and plays a
pivotal role in various cellular processes. Although there exist several computational tools to …

[HTML][HTML] Current approaches to flexible loop modeling

A Barozet, P Chacón, J Cortés - Current research in structural biology, 2021 - Elsevier
Loops are key components of protein structures, involved in many biological functions. Due
to their conformational variability, the structural investigation of loops is a difficult topic …

In silico structural analysis exploring conformational folding of protein variants in Alzheimer's disease

E Efraimidis, MG Krokidis, TP Exarchos… - International Journal of …, 2023 - mdpi.com
Accurate protein structure prediction using computational methods remains a challenge in
molecular biology. Recent advances in AI-powered algorithms provide a transformative …

[HTML][HTML] Deep learning approaches for conformational flexibility and switching properties in protein design

LSP Rudden, M Hijazi, P Barth - Frontiers in Molecular Biosciences, 2022 - frontiersin.org
Following the hugely successful application of deep learning methods to protein structure
prediction, an increasing number of design methods seek to leverage generative models to …

Revolutionizing biological science: The synergy of genomics in health, bioinformatics, agriculture, and artificial intelligence

A Biswas, A Kumari, DS Gaikwad… - OMICS: A Journal of …, 2023 - liebertpub.com
With climate emergency, COVID-19, and the rise of planetary health scholarship, the binary
of human and ecosystem health has been deeply challenged. The interdependence of …

[HTML][HTML] Protein subcellular localization prediction tools

M Gillani, G Pollastri - Computational and Structural Biotechnology Journal, 2024 - Elsevier
Protein subcellular localization prediction is of great significance in bioinformatics and
biological research. Most of the proteins do not have experimentally determined localization …