International journal of biological macromolecules
Jul 23, 2025
Targeting distal mutations holds promising implications for enzyme engineering. Here, we present an open-source computational workflow designed to explore the functional impact of distal sites, demonstrated on an artificial enzyme built on the widely...
Accurate dynamic protein structures are essential for drug design. NMR experiments can detect protein structures and potential dynamics, but the spectrum assignment and structure determination requires expertise and is time-consuming, while deep-lear...
The potential for food contact chemicals to disrupt genetic programs in development and metabolism raises concerns. Nuclear receptors (NRs) control many of these programs, and the retinoid-X receptor (RXR) is a DNA-binding partner for one-third of th...
Journal of chemical information and modeling
Jul 17, 2025
With the advancement of artificial intelligence-embedded methodologies, their application to predict fundamental molecular properties has become increasingly prevalent. In this study, a graph convolutional neural network fingerprint-enabled artificia...
Journal of chemical information and modeling
Jul 16, 2025
Scoring biomolecular complexes remains central to structural modeling efforts. Recent studies suggest that AlphaFold (AF) - a revolutionary deep learning model for biomolecular structure prediction - has implicitly learned an approximate biophysical ...
Antibodies recognize antigens via complementary and structurally dependent mechanisms. Therefore, inclusion of antibody inputs is crucial for accurate epitope prediction. Given the limited availability of antibody-antigen complex structures, any epit...
Journal of bioscience and bioengineering
Jul 10, 2025
The construction of small proteins by removing amino acid subsequences that are not involved in function, activity, or structure is crucial for bioprocessing and drug development. Traditional design methods often focus on reconstructing functional mo...
Iron is an essential nutrient for most bacteria and is often growth-limiting during infection, due to the host sequestering free iron as part of the innate immune response. To obtain the iron required for growth, many bacterial pathogens encode trans...
Journal of chemical information and modeling
Jul 8, 2025
Accurately resolving a three-dimensional structure that corresponds to an experimental mass spectrometry (MS) result is valuable for outcomes such as improved analyte identification, determination of physiochemical properties relating to conformation...
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