Biochemical and biophysical research communications
May 12, 2025
Molecular surface analysis can provide a high-dimensional, rich representation of molecular properties and interactions, which is crucial for enabling powerful predictive modeling and rational molecular design across diverse scientific and technologi...
The human CHCHD4 protein, which is a prototypical family member, carries a coiled-coil-helix-coiled-coil-helix motif that is stabilized by two disulfide bonds. Using its CPC sequence motif, CHCHD4 plays a key role in mitochondrial metabolism, cell su...
With a burgeoning number of artificial intelligence (AI) applications in various fields, biomolecular science has also given a big welcome to advanced AI techniques in recent years. In this broad field, scoring a protein-ligand binding structure to o...
Protein science : a publication of the Protein Society
May 1, 2025
Deep learning methods have played an increasingly pivotal role in advancing side-chain packing and mutation effect prediction (ΔΔG) for protein complexes. Although these two tasks are inherently closely related, they are typically treated separately ...
Invariant molecular representation models provide potential solutions to guarantee accurate prediction of molecular properties under distribution shifts out-of-distribution (OOD) by identifying and leveraging invariant substructures inherent to the m...
Even with the significant advances of AlphaFold-Multimer (AF-Multimer) and AlphaFold3 (AF3) in protein complex structure prediction, their accuracy is still not comparable with monomer structure prediction. Efficient and effective quality assessment ...
Feature attribution methods from explainable artificial intelligence (XAI) provide explanations of machine learning models by quantifying feature importance for predictions of test instances. While features determining individual predictions have fre...
MOTIVATION: Identifying antibody binding sites, is crucial for developing vaccines and therapeutic antibodies, processes that are time-consuming and costly. Accurate prediction of the paratope's binding site can speed up the development by improving ...
Protein science : a publication of the Protein Society
Feb 1, 2025
Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression...
Protein science : a publication of the Protein Society
Feb 1, 2025
Protein structure holds immense potential for pathogenicity prediction, albeit structure-based predictors are limited compared to the sequence-based counterparts due to the "structure knowledge gap" between large number of available protein sequences...
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