Biomolecular dynamics simulation is a fundamental technology for life sciences research, and its usefulness depends on its accuracy and efficiency. Classical molecular dynamics simulation is fast but lacks chemical accuracy. Quantum chemistry methods...
International journal of molecular sciences
Nov 5, 2024
Thermophilic proteins maintain their stability and functionality under extreme high-temperature conditions, making them of significant importance in both fundamental biological research and biotechnological applications. In this study, we developed a...
Angewandte Chemie (International ed. in English)
Nov 4, 2024
Designing sequences for specific protein backbones is a key step in creating new functional proteins. Here, we introduce GeoSeqBuilder, a deep learning framework that integrates protein sequence generation with side chain conformation prediction to p...
The identification of protein binding residues is essential for understanding their functions in vivo. However, it remains a computational challenge to accurately identify binding sites due to the lack of known residue binding patterns. Local residue...
Journal of chemical information and modeling
Nov 1, 2024
In the realm of biomedical research, understanding the intricate structure of proteins is crucial, as these structures determine how proteins function within our bodies and interact with potential drugs. Traditionally, methods like X-ray crystallogra...
The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and functional contexts. Identifying domains can enabl...
The accuracy of the information in the Protein Data Bank (PDB) is of great importance for the myriad downstream applications that make use of protein structural information. Despite best efforts, the occasional introduction of errors is inevitable, e...
The purpose of this review is two-fold: (1) to summarize artificial intelligence and machine learning approaches and document the role of ligand-protein structures in directing drug discovery; (2) to present examples of drugs from the recent literatu...
International journal of biological macromolecules
Oct 28, 2024
Protein-protein/peptide interactions play crucial roles in various biological processes. Exploring their interactions attracts wide attention. However, accurately predicting their binding sites remains a challenging task. Here, we develop an effectiv...
Journal of computational biology : a journal of computational molecular cell biology
Oct 23, 2024
De novo protein sequencing is an important problem in proteomics, playing a crucial role in understanding protein functions, drug discovery, design and evolutionary studies, etc. Top-down and bottom-up tandem mass spectrometry are popular approaches ...
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