Significant research progress has been made in the field of protein structure and fitness prediction. Particularly, single-sequence-based structure prediction methods like ESMFold and OmegaFold achieve a balance between inference speed and prediction...
Chemical structures of protein surfaces govern intermolecular interaction, and protein functions include specific molecular recognition, transport, self-assembly, etc. Therefore, the relationship between the chemical structure and protein functions p...
Journal of computer-aided molecular design
Aug 20, 2024
The development of novel therapeutic proteins is a lengthy and costly process, with an average attrition rate of 91% (Thomas et al. Clinical Development Success Rates and Contributing Factors 2011-2020, 2021). To increase the probability of success a...
Journal of computer-aided molecular design
Aug 16, 2024
Enhancing virtual screening enrichment has become an urgent problem in computational chemistry, driven by increasingly large databases of commercially available compounds, without a commensurate drop in in vitro screening costs. Docking these large d...
Journal of chemical information and modeling
Aug 13, 2024
Drug-Target Interaction (DTI) prediction facilitates acceleration of drug discovery and promotes drug repositioning. Most existing deep learning-based DTI prediction methods can better extract discriminative features for drugs and proteins, but they ...
IEEE/ACM transactions on computational biology and bioinformatics
Aug 8, 2024
In biochemistry, graph structures have been widely used for modeling compounds, proteins, functional interactions, etc. A common task that divides these graphs into different categories, known as graph classification, highly relies on the quality of ...
IEEE/ACM transactions on computational biology and bioinformatics
Aug 8, 2024
Drug target interaction prediction is a crucial stage in drug discovery. However, brute-force search over a compound database is financially infeasible. We have witnessed the increasing measured drug-target interactions records in recent years, and t...
Ligand binding site prediction is a crucial initial step in structure-based drug discovery. Although several methods have been proposed previously, including those using geometry based and machine learning techniques, their accuracy is considered to ...
Journal of chemical information and modeling
Aug 1, 2024
Protein engineering through directed evolution and (semi)rational approaches is routinely applied to optimize protein properties for a broad range of applications in industry and academia. The multitude of possible variants, combined with limited scr...
International journal of molecular sciences
Aug 1, 2024
Protein structure prediction is important for understanding their function and behavior. This review study presents a comprehensive review of the computational models used in predicting protein structure. It covers the progression from established pr...