Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors

We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRID. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3D database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.     

CAST/CNMR: highly accurate C NMR chemical shift prediction system considering stereochemistry

Accurate, practical prediction of ¹³C NMR chemical shifts has been achieved with a new system, CAST/CNMR, taking account of stereochemistry. The CAST/CNMR system has solved the critical problem of the accurate distinction of differences and similarities in stereochemical structures around a specific carbon, which has not yet been achieved by any other database-oriented system for prediction of ¹³C NMR chemical shifts. CAST/CNMR uses a three-dimensional structural database together with a ¹³C NMR spectral database. Absolute/relative configurational and conformational structural information are described by the CAST (CAnonical-representation of STereochemistry) coding method. This paper provides an overview of the CAST/CNMR system, and describes its application to two natural products as examples.     

The Cambridge Structural Database in Retrospect and Prospect

The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal–organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700 000 structures and is a comprehensive and fully retrospective historical archive of small‐molecule crystallography. Nearly 40 000 new structures are added each year. As X‐ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self‐financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC’s funding model in relation to open access and open data paradigms.     

地球化学模拟在高放废物地质处置中的应用与发展

随着核能事业的发展,高放废物的处理和处置问题日益突出.其中,研究高放废物在环境介质中的吸附、扩散和迁移行为是获取放射性核素对周围环境和人群健康影响的基础参数的最重要和最直接的途径.近年来,人们利用已有的实验数据及核素的基础热力学和动力学数据,附以相应的数学模型,建立了一些地球化学模拟软件,用于分析核素在地质介质中可能发生的连续性和长期性变化.目前,国内外常用的地球化学模拟软件有十多种.本文从热力学平衡计算原理、种态分布计算方法和表面配位模型假设等几个方面对地球化学模拟软件进行了简要介绍,对近年来地球化学模拟软件在核素种态分布计算和表面配位模型模拟两方面的应用进行了举例分析,并以Ca-U-CO3配合物为例,说明完备的热力学数据对地球化学模拟软件发展的重要性,以期促进我国地球化学模型的应用和发展.     

Integrated Access to Genomic and Other Bioinformation: An Essential Ingredient of the Drug Discovery Process

Abstract

Due to the high rate of data production and the need of researchers to have rapid access to new data, public databases have become the major medium through which genome mapping and sequencing data as well as macromolecular structural data are published. There are now more than 250 databases of biomolecular, structural, genetic, or phenotypic data, many of which are doubling in size annually. These databases, many of which were created and are maintained by experimentalists for their own research use, provide valuable collections of organized, validated data. However, the very number and diversity of databases now make efficient data resource discovery as important as effective data resource use. Existing autonomous biological databases contain related data which are more valuable when interconnected than when isolated. Political and scientific realities dictate that these databases will be built by different teams, in different locations, for different purposes, and using different data models and supporting DBMSs. As a consequence, connecting the related data they contain is not straightforward. Experience with existing biological databases indicates that it is possible to form useful queries across these databases, but that doing so usually requires expertise in the semantic structure of each source database. Advancing to the next level of integration among biological information resources poses significant technical and sociological challenges.     

Survey study and experimental investigation on the local behavior of pedestrian groups

Current research on pedestrian dynamics mainly focuses on the interactions among isolated individuals, the impact of the presence of groups is not fully considered. In recent 5 years, researchers have started to investigate pedestrian group movement. The aim of this work is to explore the local behavior of pedestrian groups by questionnaires and field observation. Survey study focused on pedestrians' psychology when walking in groups, which included five parts: group size, interpersonal distance, spatial relationship among group members, speed adjustment of group members, information transmission, and acid action among group members. Meantime a field observation was carried out to study group movement characteristics, which contained speed, step frequency, offset angle and interpersonal distance. The survey results show that group members have a closer interpersonal distance, faster information transmission and plenty of acid action. Conversely, group walking has a negative influence on pedestrian's speed, step frequency by comparing with the way isolated pedestrian walks. In addition, it is found that for a certain group, the group members are able to keep movement consistent. Also there exists obvious movement diversity among different group types (male dyads, female dyads, couple groups, and ordinary‐friend groups) because of different gender and social relationship. Ultimately the results will be more promising for helping to model the movement of pedestrian groups. © 2014 Wiley Periodicals, Inc. Complexity 20: 87–97, 2015     

Identification of a Prenyl Chalcone as a Competitive Lipoxygenase Inhibitor: Screening,Biochemical Evaluation and Molecular Modeling Studies

Cyclooxygenase (COX) and lipoxygenase (LOX) are key targets for the development of new anti-inflammatory agents. LOX, which is involved in the biosynthesis of mediators in inflammation and allergic reactions, was selected for a biochemical screening campaign to identify LOX inhibitors by employing the main natural product library of Brazilian biodiversity. Two prenyl chalcones were identified as potent inhibitors of LOX-1 in the screening. The most active compound, (E)-2-O-farnesyl chalcone, decreased the rate of oxygen consumption to an extent similar to that of the positive control, nordihydroguaiaretic acid. Additionally, studies on the mechanism of the action indicated that (E)-2-O-farnesyl chalcone is a competitive LOX-1 inhibitor. Molecular modeling studies indicated the importance of the prenyl moieties for the binding of the inhibitors to the LOX binding site, which is related to their pharmacological properties.