In this paper, updated structural trees for α/β-proteins containing five- and seven-segment (α/β)-motifs are represented. Novel structural motifs occurring in some families of (α + β)- and (α/β)-proteins are also characterized. Databases of these proteins have been compiled from the Protein Data Bank (PDB) and Structural Classification of Proteins (SCOP) and the corresponding structural trees have been constructed. The classification of these proteins has been developed and organized as an extension of the PCBOST database, which is available at http://strees.protres.ru . In total, the updated Protein Classification Based on Structural Trees database contains 11 structural trees, 106 levels, 635 folds, 4911 proteins and domains, and 14,202 PDB entries.
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http://dx.doi.org/10.1080/07391102.2012.691341 | DOI Listing |
J Comput Chem
January 2025
Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil.
While established guidelines exist for chirality in tetrahedral molecules, there is a notable absence of clear rules for recognizing metal-centered chirality in higher-coordination complexes. We develop decision trees to assess the likelihood of chirality-at-metal in coordination complexes with coordination numbers 4-9 with mono and bidentate ligands. Using binary decision rules based on shape, ligand type, and quantity, the trees classify complexes as chiral or achiral.
View Article and Find Full Text PDFElucidating ancestry-specific structures in admixed populations is crucial for comprehending population history and mitigating confounding effects in genome-wide association studies. Existing methods for elucidating the ancestry-specific structures generally rely on frequency-based estimates of genetic relationship matrix (GRM) among admixed individuals after masking segments from ancestry components not being targeted for investigation. However, these approaches disregard linkage information between markers, potentially limiting their resolution in revealing structure within an ancestry component.
View Article and Find Full Text PDFBMC Plant Biol
January 2025
State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China.
The slope aspect is an important environmental factor, which can indirectly change the acceptable solar radiation of forests. However, the mechanism of how this aspect changes the underground ecosystem and thus affects the growth of aboveground trees is not clear. In this study, Pinus yunnanensis plantation was taken as the research object, and the effects of soil and microbial characteristics on tree growth under different slope aspects and soil depths were systematically analyzed.
View Article and Find Full Text PDFSci Data
January 2025
Key Laboratory of Humid Subtropical Eco-Geographical Process of Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350117, China.
Deforestation-induced forest loss largely affects both the carbon budget and ecosystem services. Subsequent forest regrowth plays a crucial role in ecosystem restoration and carbon replenishment. However, there is an absence of comprehensive datasets explicitly delineating the forest regrowth following deforestation.
View Article and Find Full Text PDFCurr Biol
January 2025
Department of Coevolution of Land Use and Urbanisation, Max Planck Institute of Geoanthropology, 07745 Jena, Germany; Department of Archaeology, Max Planck Institute of Geoanthropology, 07745 Jena, Germany; School of Archaeology, University of the Philippines, Quezon City 1101, the Philippines. Electronic address:
The Amazon rainforest is characterized by a limited number of hyperdominant trees that play an oversized role in its ecosystems, nutrient cycle, and rainfall production. Some of these, such as the Brazil nut, appear to have been intensively exploited and dispersed by Indigenous populations since their earliest arrival in this part of South America around 13,000 years ago. However, the genetic diversity-and geographic structure-of these species remains poorly understood, as does their exact relationship with past human land use.
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