We have exactly enumerated all sequences and conformations of hydrophobic-polar (HP) proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the HP model, where only two types of monomers are distinguished, we determined and statistically analyzed designing sequences, i.e., sequences that have a nondegenerate ground state. Furthermore we were interested in characteristic thermodynamic properties of HP proteins with designing sequences. In order to be able to perform these exact studies, we applied an efficient enumeration method based on contact sets.
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http://dx.doi.org/10.1063/1.1814941 | DOI Listing |
J Clin Endocrinol Metab
January 2025
IMAGINE Institute Affiliate, INSERM U1163, Paris, France.
Context: Congenital hypothyroidism (CH) is the most common neonatal endocrine disorder and is chiefly caused by thyroid dysgenesis (CHTD). The inheritance mode of the disease remains complex.
Objectives: Gain insight into the inheritance mode of CHTD.
J Med Chem
January 2025
Hangzhou Carbonsilicon AI Technology Company Limited, Hangzhou 310018, Zhejiang, China.
Applying artificial intelligence techniques to flexibly model the binding between the ligand and protein has attracted extensive interest in recent years, but their applicability remains improved. In this study, we have developed CarsiDock-Flex, a novel two-step flexible docking paradigm that generates binding poses directly from predicted structures. CarsiDock-Flex consists of an equivariant deep learning-based model termed CarsiInduce to refine ESMFold-predicted protein pockets with the induction of specific ligands and our existing CarsiDock algorithm to redock the ligand into the induced binding pockets.
View Article and Find Full Text PDFPLoS One
January 2025
Washington University School of Medicine, NeuroGenomics and Informatics Center, St. Louis, MO, United States of America.
Case-only designs in longitudinal cohorts are a valuable resource for identifying disease-relevant genes, pathways, and novel targets influencing disease progression. This is particularly relevant in Alzheimer's disease (AD), where longitudinal cohorts measure disease "progression," defined by rate of cognitive decline. Few of the identified drug targets for AD have been clinically tractable, and phenotypic heterogeneity is an obstacle to both clinical research and basic science.
View Article and Find Full Text PDFPLoS One
January 2025
Department of Obstetrics and Gynaecology, Erasmus Medical Centre Rotterdam, Rotterdam, The Netherlands.
Introduction: Placental DNA methylation differences have been associated with timing in gestation and pregnancy complications. Maternal cell-free DNA (cfDNA) partly originates from the placenta and could enable the minimally invasive study of placental DNA methylation dynamics. We will for the first time longitudinally investigate cfDNA methylation during pregnancy by using Methylated DNA Sequencing (MeD-seq), which is compatible with low cfDNA levels and has an extensive genome-wide coverage.
View Article and Find Full Text PDFPLoS One
January 2025
Department of Orthopedics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Ratchathewi, Bangkok, Thailand.
Among control methods for robotic exoskeletons, biologically inspired control based on central pattern generators (CPGs) offer a promising approach to generate natural and robust walking patterns. Compared to other approaches, like model-based and machine learning-based control, the biologically inspired control provides robustness to perturbations, requires less computational power, and does not need system models or large learning datasets. While it has shown effectiveness, a comprehensive evaluation of its user experience is lacking.
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