AIMC Topic: Models, Molecular

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DihedralsDiff: A Diffusion Conformation Generation Model That Unifies Local and Global Molecular Structures.

Journal of chemical information and modeling
Significant advancements have been made in utilizing artificial intelligence to learn to generate molecular conformations, which has greatly facilitated the discovery of drug molecules. In particular, the rapid development of diffusion models has led...

Structural Biology in the AlphaFold Era: How Far Is Artificial Intelligence from Deciphering the Protein Folding Code?

Biomolecules
Proteins are biomolecules characterized by uncommon chemical and physicochemical complexities coupled with extreme responsiveness to even minor chemical modifications or environmental variations. Since the shape that proteins assume is fundamental fo...

M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.

BMC bioinformatics
BACKGROUND: Association and cooperation among structural domains play an important role in protein function and drug design. Despite remarkable advancements in highly accurate single-domain protein structure prediction through the collaborative effor...

Machine learning models for predicting configuration of modified knuckle epitope peptides of BMP-2 protein using mesoscale simulation data.

Physical chemistry chemical physics : PCCP
The high doses of bone morphogenetic proteins (BMPs) cause undesired side effects in skeletal tissue regeneration. An alternative approach is to use the bioactive knuckle epitope domain of BMP-2 (BMP2-KEP) with an open-arm structure as part of the pr...

Artificial intelligence for RNA-ligand interaction prediction: advances and prospects.

Drug discovery today
Accurate prediction of RNA-ligand interactions is vital for understanding biological processes and advancing RNA-targeted drug discovery. Given their complexity, artificial intelligence (AI) is revolutionizing the study of RNA-ligand interactions, of...

Titania: an integrated tool for in silico molecular property prediction and NAM-based modeling.

Molecular diversity
Advances in drug discovery and material design rely heavily on in silico analysis of extensive compound datasets and accurate assessment of their properties and activities through computational methods. Efficient and reliable prediction of molecular ...

Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network.

Cell
In humans, selective and promiscuous interactions between 46 secreted chemokine ligands and 23 cell surface chemokine receptors of the G-protein-coupled receptor (GPCR) family form a complex network to coordinate cell migration. While chemokines and ...

A hybrid variational autoencoder and WGAN with gradient penalty for tertiary protein structure generation.

Scientific reports
Elucidating the tertiary structure of proteins is important for understanding their functions and interactions. While deep neural networks have advanced the prediction of a protein's native structure from its amino acid sequence, the focus on a singl...

The prediction of RNA-small molecule binding sites in RNA structures based on geometric deep learning.

International journal of biological macromolecules
Biological interactions between RNA and small-molecule ligands play a crucial role in determining the specific functions of RNA, such as catalysis and folding, and are essential for guiding drug design in the medical field. Accurately predicting the ...

Emerging frontiers in protein structure prediction following the AlphaFold revolution.

Journal of the Royal Society, Interface
Models of protein structures enable molecular understanding of biological processes. Current protein structure prediction tools lie at the interface of biology, chemistry and computer science. Millions of protein structure models have been generated ...