Crystallographic software: a sustainable resource for the community.

Methods Mol Biol

Department of Biochemistry, University of Vermont, Burlington, VT, USA.

Published: December 2007

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.

Download full-text PDF

Source
http://dx.doi.org/10.1385/1-59745-266-1:273DOI Listing

Publication Analysis

Top Keywords

crystallographic software
8
software sustainable
4
sustainable resource
4
resource community
4
community virtually
4
virtually software
4
software constantly
4
constantly changing
4
changing evolving
4
evolving crystallographic
4

Similar Publications

Virtual Screening Identifies Inhibitors of SARS-CoV-2 Main Protease through Pharmacophore and Similarity Approaches.

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.

View Article and Find Full Text PDF
Article Synopsis
  • Microcrystal electron diffraction (MicroED) is an advanced structural method useful for analyzing a variety of samples, including small molecules and proteins, using cryogenic electron microscopy techniques.
  • The method captures diffraction data through the continuous rotation of small 3D crystals while being observed by a high-speed camera, then utilizes X-ray crystallographic software for structure determination.
  • This guide provides detailed protocols for preparing samples, emphasizing that individual crystals need tailored growth conditions, and aids those with backgrounds in biochemistry and crystallography in optimizing their MicroED experiments, which can take from one day to several weeks.
View Article and Find Full Text PDF

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 PDF

Prediction of ADN/ANF cocrystal and its theoretical properties.

J 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 PDF

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.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!