Virtually all software is constantly changing and evolving (and crystallographic software is no exception), which makes it nearly impossible to write a chapter that will remain current. In this chapter, we introduce CRYSTAL, a website (http://crystal.uvm.edu) where a comprehensive list of available crystallographic packages for each step of macromolecular structure determination will be maintained. Additionally, we provide links to books, journals, and a number of educational sites on crystallography. For each program/site included at CRYSTAL, a detailed description will include: the most current version, the authors, and appropriate operating systems to host the program. Links to download the programs, available tutorials, and references to cite when using the program/site are also provided.
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http://dx.doi.org/10.1385/1-59745-266-1:273 | DOI Listing |
Curr Pharm Des
January 2025
Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, P.O Box 13140, Amman 11942, Jordan.
Introduction: The emergence of SARS-CoV-2 and the COVID-19 pandemic highlighted the urgent need for novel antiviral therapies. The main protease (Mpro) of SARS-CoV-2 is a key enzyme in viral replication and a promising therapeutic target.
Methods: This study employed virtual screening approaches to identify potential Mpro inhibitors, leveraging both structure- and ligand-based methods.
Nat Protoc
December 2024
Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA.
Int J Mol Sci
November 2024
Biodiversity and Biotechnology Bionorte Network, Federal University of Para, Belém 66075-110, PA, Brazil.
Naphthoquinones eleutherin and isoeleutherin have demonstrated promising antibacterial activity, probably due to their quinone structure, which can generate reactive oxygen species. The study examines the activities of pathogens, such as and , associated with antimicrobial resistance and explores their potential mechanisms of action. The MIC, IC, and MBC were determined.
View Article and Find Full Text PDFJ Mol Model
December 2024
State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
Context: Ammonium dinitramide (ADN) is highly hygroscopic, which poses significant challenges in its practical applications. Consequently, mitigating this hygroscopic nature has been a primary focus in the research and development of ADN. This study investigated the properties of the ADN/3-amino-4-nitrofurazan (ANF) cocrystal using density functional theory, molecular dynamics, and Monte Carlo methods.
View Article and Find Full Text PDFJ Comput Aided Mol Des
December 2024
University of Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany.
Although small molecule superposition is a standard technique in drug discovery, a rigorous performance assessment of the corresponding methods is currently challenging. Datasets in this field are sparse, small, tailored to specific applications, unavailable, or outdated. The newly developed LOBSTER set described herein offers a publicly available and method-independent dataset for benchmarking and method optimization.
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