We present a formalism of a neural network encoding bonded interactions in molecules. This intramolecular encoding is consistent with the models of intermolecular interactions previously designed by this group. Variants of the encoding fed into a cor...
Journal of chemical information and modeling
Oct 26, 2023
Small-molecule conformer generation (SMCG) is an extremely important task in both ligand- and structure-based computer-aided drug design, especially during the hit discovery phase. Recently, a multitude of artificial intelligence (AI) models tailored...
Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence (AI) have a burgeoning synergy. Deep learning-based structural predictors have forever changed structural biology, yet these tools currently face limitations in ac...
Highly effective de novo design is a grand challenge of computer-aided drug discovery. Practical structure-specific three-dimensional molecule generations have started to emerge in recent years, but most approaches treat the target structure as a con...
The organisation of the genome in nuclear space is an important frontier of biology. Chromosome conformation capture methods such as Hi-C and Micro-C produce genome-wide chromatin contact maps that provide rich data containing quantitative and qualit...
Machine-learning-based scoring functions (MLSFs) have gained attention for their potential to improve accuracy in binding affinity prediction and structure-based virtual screening (SBVS) compared to classical SFs. Developing accurate MLSFs for SBVS r...
Journal of chemical information and modeling
Jun 12, 2023
Molecular dynamics simulation is an indispensable tool for understanding the collective behavior of atoms and molecules and the phases they form. Statistical mechanics provides accurate routes for predicting macroscopic properties as time-averages ov...
Proceedings of the National Academy of Sciences of the United States of America
May 30, 2023
Protein side-chain packing (PSCP), the task of determining amino acid side-chain conformations given only backbone atom positions, has important applications to protein structure prediction, refinement, and design. Many methods have been proposed to ...
FSATOOL is an integrated molecular simulation and data analysis program. Its old molecular dynamics engine only supports simulations in vacuum or implicit solvent. In this work, we implement the well-known smooth particle mesh Ewald method for simula...
Accurate conformational energetics of molecules are of great significance to understand maby chemical properties. They are also fundamental for high-quality parameterization of force fields. Traditionally, accurate conformational profiles are obtaine...
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