We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac.
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http://dx.doi.org/10.1002/jcc.21388 | DOI Listing |
Chem Biodivers
January 2025
Universidad Nacional del Litoral Facultad de Bioquimica y Ciencias Biologicas, Química Orgánica, Ciudad Universitaria. Paraje el Pozo S/N, Argentina, 3000, Santa Fe, ARGENTINA.
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has highlighted the urgent need for novel therapeutic agents targeting viral enzymes such as the main protease (Mpro), which plays a crucial role in viral replication. In this study, we investigate the inhibitory potential of 23 peptides isolated from the skin of amphibians belonging to the Hylidae and Leptodactylidae families against SARS-CoV-2 Mpro. Five peptides demonstrated significant inhibition using a colorimetric Mpro inhibition assay, with IC50 values ranging from 41 to 203 µM.
View Article and Find Full Text PDFJ Org Chem
January 2025
Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, Bielefeld 33615, Germany.
Spin labels based on Gd complexes are important tools for the elucidation of the structure, dynamics and interaction of biomolecules by electron paramagnetic resonance (EPR) spectroscopy. Their EPR spectroscopic properties line width and relaxation times influence their performance in a particular application. To be able to apply a complex well-suited for a specific application, a set of Gd complexes with different EPR spectroscopic properties ready-made for spin labeling will be highly useful.
View Article and Find Full Text PDFPLoS One
January 2025
School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia.
The cytotoxic T-lymphocyte antigen-4 (CTLA4) is essential in controlling T cell activity within the immune system. Thus, uncovering the molecular dynamics of single nucleotide polymorphisms (SNPs) within the CTLA4 gene is critical. We identified the non-synonymous SNPs (nsSNPs), examined their impact on protein stability, and identified the protein sequences associated with them in the human CTLA4 gene.
View Article and Find Full Text PDFPLoS Comput Biol
January 2025
Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, United States of America.
Negotiating social dynamics among allies and enemies is a complex problem that often requires individuals to tailor their behavioral approach to a specific situation based on environmental and/or social factors. One way to make these contextual adjustments is by arranging behavioral output into intentional patterns. Yet, few studies explore how behavioral patterns vary across a wide range of contexts, or how allies might interlace their behavior to produce a coordinated response.
View Article and Find Full Text PDFSci Adv
January 2025
Institute of Zoology, University of Cologne, Cologne, Germany.
Some unique asexual species persist over time and contradict the consensus that sex is a prerequisite for long-term evolutionary survival. How they escape the dead-end fate remains enigmatic. Here, we generated a haplotype-resolved genome assembly on the basis of a single individual and collected genomic data from worldwide populations of the parthenogenetic diploid oribatid mite to identify signatures of persistence without sex.
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