Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3D atomic models of biological molecules. AlphaFold-predicted models generate initial 3D coordinates; however, model inaccuracy and conformational heterogeneity o...
Modern semiempirical electronic structure methods have considerable promise in drug discovery as universal "force fields" that can reliably model biological and drug-like molecules, including alternative tautomers and protonation states. Herein, we c...
The rapid progress of machine learning (ML) in predicting molecular properties enables high-precision predictions being routinely achieved. However, many ML models, such as conventional molecular graph, cannot differentiate stereoisomers of certain t...
Combinatorial chemistry & high throughput screening
Jan 1, 2023
With the continuous development of structural biology, the requirement for accurate threedimensional structures during functional modulation of biological macromolecules is increasing. Therefore, determining the dynamic structures of bio-macromolecul...
The ability to identify antigenic determinants of pathogens, or epitopes, is fundamental to guide rational vaccine development and immunotherapies, which are particularly relevant for rapid pandemic response. A range of computational tools has been d...
MOTIVATION: Co-evolution analysis can be used to accurately predict residue-residue contacts from multiple sequence alignments. The introduction of machine-learning techniques has enabled substantial improvements in precision and a shift from predict...
The superior performance of machine-learning scoring functions for docking has caused a series of debates on whether it is due to learning knowledge from training data that are similar in some sense to the test data. With a systematically revised met...
Biomacromolecules manifest dynamic conformational fluctuation and involve mutual interconversion among metastable states. A robust mapping of their conformational landscape often requires the low-dimensional projection of the conformational ensemble ...
MOTIVATION: Geometry-based properties and characteristics of drug molecules play an important role in drug development for virtual screening in computational chemistry. The 3D characteristics of molecules largely determine the properties of the drug ...
Three-dimensional (3D) architecture of the chromosomes is of crucial importance for transcription regulation and DNA replication. Various high-throughput chromosome conformation capture-based methods have revealed that CTCF-mediated chromatin loops a...
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