A marine natural product database

A database of marine natural products has been developed. The database contains approximately 6000 chemical compounds derived from over 10,000 marine-derived materials. For each compound, the structure, physical and chemical properties, marine source, and biological activities are given. A computer program for searching this database has also been developed and is described.     

A database for QA/QC in neutron activation analysis and gamma-ray spectrometry

A database has been designed for storing, retrieving and analyzing information about samples, experimental conditions and results obtained by neutron activation analysis and gamma-ray spectrometry. It has been created using Microsoft ACCESS 2002 under a Windows operating system. The database has been designed not only for saving information but also for quality assurance and quality control purposes. The structure of the relational design has been discussed and demonstrated with a new graphical feature of ACCESS 2002 called PIVOTCHART.     

Toward creation of a universal NMR database for the stereochemical assignment of acyclic compounds: proof of concept

[formula: see text] Using the C.5-C.10 portion of the oasomycin class of natural products, the reliability and usefulness of an NMR database for the stereochemical assignment of acyclic compounds has been demonstrated. The predicted relative stereochemistry based on the NMR database has unambiguously been established via synthesis.     

开放骨架磷酸铝合成反应数据库的建立与应用（I）

本文介绍了开放骨架磷酸铝合成反应数据库的建立、收录的数据资料信息和数据库的检索查询方法,并对该数据库就骨架元素组成、反应产物的结构维数、孔道环数、合成所用的有机模板剂等方面做了统计分析．磷酸铝合成反应数据库的建立对于微孔功能体系的分子工程学研究提供了重要的基础数据．     

New approach to molecular docking and its application to virtual screening of chemical databases

This paper describes the validation of a molecular docking method and its application to virtual database screening. The code flexibly docks ligand molecules into rigid receptor structures using a tabu search methodology driven by an empirically derived function for estimating the binding affinity of a protein-ligand complex. The docking method has been tested on 70 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. The lowest energy geometry produced by the docking protocol is within 2.0 A root mean square of the experimental binding mode for 79% of the complexes. The method has been applied to the problem of virtual database screening to identify known ligands for thrombin, factor Xa, and the estrogen receptor. A database of 10,000 randomly chosen "druglike" molecules has been docked into the three receptor structures. In each case known receptor ligands were included in the study. The results showed good separation between the predicted binding affinities of the known ligand set and the database subset.     

Enabling the exploration of biochemical pathways

The Biochemical Pathways Wall Chart (http://www.expasy.org/tools/pathways/ref.1) has been converted into a molecule and reaction database. Major features of this database are that each molecule is represented by lists of all atoms and bonds (as connection tables), and in the reactions the reaction centre, the atoms and bonds directly involved in the bond rearrangement process, are marked. The information in the database has been enriched by a set of diverse 3D structure conformations generated by the programs CORINA and ROTATE. The web-based structure and reaction retrieval system C@ROL provides a wide range of search methods to mine this rich database. The database is accessible at http://www2.chemie.uni-erlangen.de/services/biopath/index.html and http://www.mol-net.de/databases/biopath.html .     

Development of a database of gas chromatographic retention properties of organic compounds

A comprehensive database of gas chromatographic retention properties of chemical compounds has been developed using multiple literature sources. The National Institute of Standards and Technology (NIST) database of retention data for non-polar and polar stationary phases currently contains 292,924 data records for 42,888 compounds. The database includes data for Kováts indices, linear indices, Lee indices, retention times and retention volumes. The first release of this database for non-polar stationary phases is available with NIST/US Environmental Protection Agency (EPA)/National Institutes of Health (NIH) Mass Spectral Database (June 2005) and through the internet (NIST Chemistry WebBook). The paper describes the database and the process by which it has been compiled. The format of data presentation and the quality control procedures are described. Data sources of gas chromatographic retention data are also discussed.     

Automation of analysis of airborne radionuclides observed in Canadian CTBT radiological monitoring networks using LINSSI

Linux System for Spectral Information (LINSSI¹) is a SQL database and established under Linux. Currently it is compatible with HPGe gammaspectra analysis software UniSampo, Shaman and Aatami. Based on this database and software, an automated analysis pipeline has been setup for Canadian CTBT radiological monitoring networks. This paper has investigated the performance of this pipeline in its capabilities and reliabilities of rapid small peak search, nuclide identification, and radionuclide activity concentration evaluation. Up to now, more than 80 thousand daily monitoring gamma-spectra have been automatically received and processed, the results have been stored in database. The pipeline nuclide detection limits is satisfied for environmental radiation monitoring and nuclear emergency preparedness.     

Visualization and substructure retrieval tools in the MOGADOC database (molecular gasphase documentation)

Over the years the MOGADOC database, which covers the literature for gas-phase electron diffraction, microwave spectroscopy, and molecular radio astronomy from the inception of each method, has been developed. Recently visualization and substructure retrieval tools have been implemented. New features are described by means of typical database applications.     

中药材全息指纹谱图库的建立

 设计并建立了中药材全息指纹谱图库软件 ,用于存放各种指纹谱及其相关信息。该数据库将为中药分析及其质量控制提供帮助与参考。     

Recovery of plutonium from aqueous waste solutions using porous zirconia spherical particles

Based on the Linssi database and UniSampo/Shaman software, an automated analysis platform has been setup for the analysis of large amounts of gamma-spectra from the primary coolant monitoring systems of a CANDU reactor. Thus, a database inventory of gaseous and volatile fission products in the primary coolant of a CANDU reactor has been established. This database is comprised of 15,000 spectra of radioisotope analysis records. Records from the database inventory were retrieved by a specifically designed data-mining module and subjected to further analysis. Results from the analysis were subsequently used to identify the reactor coolant half-life of ¹³⁵Xe and ¹³³Xe, as well as the correlations of ¹³⁵Xe and ⁸⁸Kr activities.     

On-line FT-Raman and dispersive Raman spectra database of artists’ materials (e-VISART database)

Raman spectroscopy has been widely applied in the analysis of different types of artwork. This technique is sensitive, reliable, non-destructive and can be used in situ. However, there are few references in the literature regarding specific Raman spectra libraries for the field of artwork analysis. In this paper, the development of two on-line databases with Fourier transform Raman (FT-Raman; 1064 nm) and dispersive Raman (785 nm) spectra of materials used in fine art is presented; both are implemented in the e-vibrational spectroscopic databases of artists materials database (e-VISART). The database provides not only spectra, but also information about each pigment. It must be highlighted that for each pigment or material several spectra are available from different dealers. Some of the FT-Raman spectra available in the e-VISART database have not been published until now. Some examples in which the e-VISART database has been successfully used are presented.     

PhotochemCAD 2: a refined program with accompanying spectral databases for photochemical calculations

The PhotochemCAD program has been revised extensively. Calculations can be performed using eight modules (oscillator strength, transition dipole moment and natural radiative lifetime, Förster energy transfer, multicomponent analysis, blackbody radiator, artificial spectrum creation, transmission calculation, and analysis of energy transfer among linear multichromophore arrays). The user interface has been streamlined to facilitate visual display, operation of the various modules, input of user data via a wizard and output of spectra and calculations. The database of absorption and fluorescence spectra has been expanded to 150 photochemically relevant compounds. A database of solar spectra has been added. The program runs under Windows and is equipped with extensive literature references and help features, including a tutorial section with video files.     

Luminescence database I--minerals and materials.

A luminescence database for minerals and materials has been complied from the literature, the aim being to create a resource that will aid in the analysis of luminescence spectral of ionic species in minerals and materials. The database is based on a range of excitation techniques and records both major and minor lines, and their activators. The luminescence techniques included in the database are cathodoluminescence, ion luminescence, and photoluminescence. When combined with other traditional X-ray measurements collected on the same region, use of the luminescence database will give additional insight into the chemistry of minerals and materials.     

MOGADOC (Molecular Gas Phase Documentation) — An interactive computerised search/retrieval system

For 22 years the Section for Structure Documentation (SSD), University of Ulm, has provided a documentation service covering the literature of molecules studied in the gas phase by electron diffraction, microwave spectroscopy and other techniques. Much of the information which has been accumulated over these years has now been keyboarded to constitute a computerised database. An interactive search/retrieval system, MOGADOC, has been written using the SIMULA¹ language implemented on the UNIVAC 1100/82 computer at the University of Freiburg. MOGADOC enables the user to search the database on the basis of bibliographic, chemical and physical search terms.     

A database of new zeolite-like materials

We here describe a database of computationally predicted zeolite-like materials. These crystals were discovered by a Monte Carlo search for zeolite-like materials. Positions of Si atoms as well as unit cell, space group, density, and number of crystallographically unique atoms were explored in the construction of this database. The database contains over 2.6 M unique structures. Roughly 15% of these are within +30 kJ mol(-1) Si of α-quartz, the band in which most of the known zeolites lie. These structures have topological, geometrical, and diffraction characteristics that are similar to those of known zeolites. The database is the result of refinement by two interatomic potentials that both satisfy the Pauli exclusion principle. The database has been deposited in the publicly available PCOD database and in www.hypotheticalzeolites.net/database/deem/.     

Developing an antituberculosis compounds database and data mining in the search of a motif responsible for the activity of a diverse class of antituberculosis agents

A novel data mining procedure to look for new antitubercular agents and targets as well as to find a minimum common bioactive substructure (MCBS), has been reported here. The methodology extracts MCBS, both across the diverse chemical classes and within the particular chemical class, known to be present in the various marketed drugs alongside antimycobacterial compounds with known MICs. For this purpose a small in-house database of compounds has been created, for which MICs against Mycobacterium are known. The compounds have been collected from literature available on the synthetic compounds, having known MICs against Mycobacterium tuberculosis. An elaborate HQSAR (Hologram QSAR) study has been attempted to extract active fragment from a diverse class of compounds, in combination with the clustering technique to select a homogeneous group of compounds having good a profile toward the activity. The 2D pharmacophore (the 2D fragments extracted from HQSAR) has been validated searching the database. It has been found further that this validated 2D pharmacophore could be used for searching the orphan target in Mycobacterium effectively.     

Collection and preparation of molecular databases for virtual screening

Drug discovery and development research is undergoing a paradigm shift from a linear and sequential nature of the various steps involved in the drug discovery process of the past to the more parallel approach of the present, due to a lack of sufficient correlation between activities estimated by in vitro and in vivo assays. This is attributed to the non-drug-likeness of the lead molecules, which has often been detected at advanced drug development stages. Thus a striking aspect of this paradigm shift has been early/parallel in silico prioritization of drug-like molecular databases (also database pre-processing), in addition to prioritizing compounds with high affinity and selectivity for a protein target. In view of this, a drug-like database useful for virtual screening has been created by prioritizing molecules from 36 catalog suppliers, using our recently derived binary QSAR based drug-likeness model as a filter. The performance of this model was assessed by a comparative evaluation with respect to commonly used filters implemented by the ZINC database. Since the model was derived considering all the limitations that have plagued the existing rules and models, it performs better than the existing filters and thus the molecules prioritized by this filter represent a better subset of drug-like compounds. The application of this model on exhaustive subsets of 4,972,123 molecules, many of which have passed the ZINC database filters for drug-likeness, led to a further prioritization of 2,920,551 drug-like molecules. This database may have a great potential for in silico virtual screening for discovering molecules, which may survive the later stages of the drug development research.     

航空用橡胶类材料衰减全反射法红外光谱图数据库的建立

利用衰减全反射法(ATR)制样简单、检测快捷的优点,收集已知航空用橡胶类材料牌号的ATR红外光谱图,建立ATR红外光谱图数据库,用红外光谱数据库检索方法来方便完成鉴定未知物质.