We present an open source tool able to describe intermolecular electrostatic interactions within the framework of the effective fragment potential (EFP) method. Complex molecular structure is subdivided into compact rigid fragments and parameters of their interactions are obtained from ab initio calculations. Automatic procedure allows for searching of these parameters into the existing database and merge new fragments into it. A set of standard fragments useful for the studies of organic semiconductors is also provided. Input files both for purely EFP and hybrid QM/MM calculations can be generated. The program is written in python and freely available on GitHub: https://github.com/ale-odinokov/pyEFP © 2017 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/jcc.25149 | DOI Listing |
Eur J Med Res
January 2025
Department of General, Visceral and Thoracic Surgery, German Armed Forces Central Hospital, Koblenz, Germany.
Liquid biomarkers are essential in trauma cases and critical care and offer valuable insights into the extent of injury, prognostic predictions, and treatment guidance. They can help assess the severity of organ damage (OD), assist in treatment decisions and forecast patient outcomes. Notably, small extracellular vesicles, particularly those involved in splenic trauma, have been overlooked.
View Article and Find Full Text PDFBMC Chem
January 2025
Department of Biochemistry, Faculty of Pharmacy, Adıyaman University, Adıyaman, 02000, Türkiye.
This study investigates the phenolic compounds (PC), volatile compounds (VC), and fatty acids (FA) of extra virgin olive oil (EVOO) derived from the Turkish olive variety "Sarı Ulak", along with ADMET, DFT, molecular docking, and gene network analyses of significant molecules identified within the EVOO. Chromatographic methods (GC-FID, HPLC) were employed to characterize FA, PC, and VC profiles, while quality parameters, antioxidant activities (TAC, ABTS, DPPH) were assessed via spectrophotometry. The analysis revealed a complex composition of 40 volatile compounds, with estragole, 7-hydroxyheptene-1, and 3-methoxycinnamaldehyde as the primary components.
View Article and Find Full Text PDFGenome Biol
January 2025
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, 90095, CA, USA.
Deciphering the link between tissue architecture and function requires methods to identify and interpret patterns in spatial arrangement of cells. We present SMORE, an approach to detect patterns in sequential arrangements of cells and examine their associated gene expression specializations. Applied to retina, brain, and embryonic tissue maps, SMORE identifies novel spatial motifs, including one that offers a new mechanism of action for type 1b bipolar cells.
View Article and Find Full Text PDFHereditas
January 2025
Emergency Department, Ningbo Municipal Hospital of Traditional Chinese Medicine, Affiliated Hospital of Zhejiang Chinese Medical University, Ningbo, Zhejiang Province, China.
Endometriosis is a complex gynecological condition characterized by abnormal immune responses. This study aims to explore the immunomodulatory effects of monoterpene glycosides from Paeonia lactiflora on endometriosis. Using the ssGSEA algorithm, we assessed immune cell infiltration levels between normal and endometriosis groups.
View Article and Find Full Text PDFJ Phys Chem A
January 2025
Computer Modelling Group, 3710 33 St NW, Calgary, Alberta T2L 2M1, Canada.
Coarse-grained molecular dynamics simulation is widely accepted for assessment of a large complex biological system, but it may also lead to a misleading conclusion. The challenge is to simulate protein structural dynamics (such as folding-unfolding behavior) due to the lack of a necessary backbone flexibility. This study developed a standard coarse-grained model directly from the protein atomic structure and amino acid coarse-grained FF (such as MARTINI FF v2.
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