Coarse-grained models have provided researchers with greatly improved computational efficiency in modeling structures and dynamics of biomacromolecules, but, to be practically useful, they need fast and accurate conversion methods back to the all-ato...
Efficiently predicting the paratope holds immense potential for enhancing antibody design, treating cancers and other serious diseases, and advancing personalized medicine. Although traditional methods are highly accurate, they are often time-consumi...
Journal of chemical information and modeling
39580812
Graphs are one of the most natural and powerful representations available for molecules; natural because they have an intuitive correspondence to skeletal formulas, the language used by chemists worldwide, and powerful, because they are highly expres...
Neural networks : the official journal of the International Neural Network Society
39732065
The remarkable success of Graph Neural Networks underscores their formidable capacity to assimilate multimodal inputs, markedly enhancing performance across a broad spectrum of domains. In the context of molecular modeling, considerable efforts have ...
Journal of computer-aided molecular design
39724258
Conotoxins, being small disulfide-rich and bioactive peptides, manifest notable pharmacological potential and find extensive applications. However, the exploration of conotoxins' vast molecular space using traditional methods is severely limited, nec...
Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce confo...
Journal of chemical theory and computation
39702999
Helices are important secondary structural motifs within proteins and are pivotal in numerous physiological processes. While amino acids (AA) such as alanine and leucine are known to promote helix formation, proline and glycine disfavor it. Helical s...
MOTIVATION: Accurately identifying ligands plays a crucial role in the process of structure-guided drug design. Based on density maps from X-ray diffraction or cryogenic-sample electron microscopy (cryoEM), scientists verify whether small-molecule li...
Much of the human genome is transcribed into RNAs, many of which contain structural elements that are important for their function. Such RNA molecules-including those that are structured and well-folded-are conformationally heterogeneous and flexible...
Methods in molecular biology (Clifton, N.J.)
39576578
Protein structure prediction is fundamental to molecular biology and has numerous applications in areas such as drug discovery and protein engineering. Machine learning techniques have greatly advanced protein 3D modeling in recent years, particularl...