Internet chemical structure data

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB at http //www.rcsb.org/pdb/home/home.do is the online source for X-ray and NMR structural data. Many software programs mentioned in Section 4.5 include the facihty to visualize imported data however, two free software programs operate well in this regard. One is MDL Chime described previously in this section. Chime, a chemical structure visualization plug-in for Internet Explorer and Netscape Communicator, supports a wide variety of molecule coordinate formats, including PDB (protein data bank), Molfile (from ISIS/Draw), MOP (MOPAC input hies), and GAU (Gaussian Input hies). 

Quality control is performed at the moment of data entry, in particular, with respect to errors present in publications. Chemical structures are checked for structural consistency by matching the molecular weight (MW) and chemical formula with the ones available in the experimental section and/or supporting information - whenever available, and by comparison to prior publications. Whenever in doubt, we also use other sources, such as the Merck Index [20] and free Internet resources. In the instances... 

Richard, A.M., Gold, L.S. and Nicklaus, M.C. (2006) Chemical structure indexing of toxicity data on the internet moving toward a flat world. Curr. Opin. Drug Discov. Dev., 9 (3),... 

An INTERNET compatible database for solvent extraction of metal ions (SEDATA), developed by H. Watarai et al., contains about 9,600 equilibrium constants, including distribution constants, extraction constants, and adduct formation constants, for more than 1,400 ligands and 82 metal ions.50 Raw data points of extraction curves are also incorporated to be reconstructed as a figure. However, SEDATA contains no fields for 2D chemical structures of extractants and allows one to perform a search using only eight fields (classification, metal, valence, reagent, solvent, title of the paper, author, and year). 

Solvent extraction Database (SXD) software has been developed by A. Varnek et al.51 Each record of SXD corresponds to one extraction equilibrium and contains 90 fields to store bibliographic information, system descriptions, chemical structures of extractants, and thermodynamic and kinetic data in textual, numerical, and graphical forms. A search can be performed by any field including 2D structure. SXD tools allow the user to compare plots from different records and to select a subset of data according to user-defined constraints (identical metal, content of aqueous or organic phases, etc.). This database, containing about 3,500 records, is available on the INTERNET (http //infochim.u-strasbg.fr/sxd). 

The days of the hard copy encyclopaedias of chemical information are certainly numbered. Most of the important ones are now available in CD-ROM format. The data on these CD-ROM s can be conveniently searched, in the home, the office or the laboratory making a trip to the library unnecessary. The highly important databases of international patent information are also available in the same format and also on websites via the Internet. The searching of large databases, e.g. Chemical Abstracts, by inputting chemical structures has lessened the need for an expert to come between the researcher and this information. 

Recent advances in chemoinformatics have greatly enhanced the utility of these resources and many are now accessible via the Internet.28 CHEMnet-BASE (www.chemnetbase.com) provides online access to a variety of databases including the Dictionary of Natural Products and the Dictionary of Marine Natural Products, although full access through CHEMnetBASE requires a subscription. The Chemical Structure Lookup Service (http //cactus.nci.-nih.gov/lookup) is an open access database and incorporates information from more than 80 databases on over 27 million structures. PubChem (http //pub-chem.ncbi.nlm.nih.gov/) is another open access database that also links bioassay data to each structure. Measures such as the US National Institutes of Health (NIH) Public Access Policy Mandate should increase the amount of openly accessible information available on the Internet and facilitate dissemination of information. 

Encryption. The conversion of data in a readable or decipherable code into another, possibly undecipherable, code. The most common encryption involves sensitive pieces of data like passwords and identification numbers. In chemistry, it is sometimes necessary to encrypt larger pieces of information, such as chemical structures and the results of assays—at least during passage of such information over networks or the Internet. Decryption of the information typically requires one or more keys, which are often built into the encryption and decryption software. 

For example, using the database prepared by the Chemistry Department at the University of Akron http //ull.chemistry.uakron. edu/erd/) which is considered to an academic work, the flash point of perchloroethylene is reported as 113°F. In addition the Royal Society of Chemistry s data portal Chemspider (http /AA/ww. chemspider.com/Chemical-Structure.29106.html) reports a value of 83.4°F. However, various internet sources, such as Wikipedia http //en.wikipedia.org/wiki/Fetrachloroethylene), the Center for Disease Control s Pocket Guide to Chemical Hazards (http //www. cdc.gov/niosh/npg/npgd0599.html), and most MSDSs report that the flash point value is "NA" which is presumed to mean "none."... 

Publication on the Internet offers many advantages for chemists. Documents can contain color graphics, movies, chemical structures, spectra, raw data, and so forth, most of which is difficult (if not impossible) or prohibitively expensive to include in traditional publications. The UC will publish articles in any and all areas of chemistry which take advantage of the special attributes of the Internet, The Journal will publish... 

There are two basic mechanisms for transporting a three-dimensional chemical visualization as Internet data as a file with geometric objects or as a chemical MIME structure file. MIME files have been discussed in the previous paragraphs. They offer full chemical information, but only severely limited display choices, restricted to what is available to the local helper application and which, furthermore, cannot be controlled by the author. The transport of information such as orbital shapes, other than atomic coordinates, is not possible with the standard chemical MIME formats. 

MDL Information Systems, Inc., a subsidiary of Elsevier Science, Inc., also have a free Internet access to its database of commercially available substances, claimed to contain information on more than 400,000 chemicals (available from www.mdh.com No toxicity or environmental property data are given. Similarly, the ChemBridge Corp. provides a list of over available 450,000 substances to subscribers (www.chembridge.com). Russia s ChemStar Ltd. provides a similar type of database with over 500,000 compounds available (www.chemstar.ru). The list of compounds is downloadable in structure data hie (SDF) format and is being updated regularly. 

There are several examples on the Internet of websites that are actively working toward providing free and unrestricted access to scientific data for the scientific community and general public. One of the biggest examples that is also closely related to chemistry is PubChem (http //pubchem.ncbi.nhn.nih.gov/), an online database of chemical compounds, their structures, and chemical and other related data. PubChem not only provides its data online on its webpages, but it also makes the chemical content easily accessible using automated tools (in this case, compressed SDfiles containing tens of thousands of structures each are used). 

NIST Resources. The National Institute of Standards and Technology has a Standard Reference Data Program that maintains electronic databases on Analytical chemistry, Atomic and molecular physics, Biotechnology, Chemical and crystal structure. Fluids, Materials properties. Surface data, and Thermochemical data. Some of these databases are available at moderate cost as PC products (diskettes, CD-ROMs, or Internet downloads) and some are free online systems. Further information is available on the website www. nist.gOv/srd/ begin.htm. 

If measured values are not available for the chemical of interest, a substructure search should be conducted to attempt to identify a close structural analog which has a measured value. Several options are available, a few of which allow the rapid identification of an analog with measured values. For example, there are free databases on the internet that are substructure searchable. ChemlDp/us (Table 1) is substructure searchable for all of the >6000 chemicals that are in the Hazardous Substances Data Bank (HSDB) as well as the 269 000 structures that are in the ChemlDp/us file. ChemS (Table 1) can simultaneously substructure search the 20 000 chemicals in the four files of the Environmental Fate Data Base (EFDB) [4,5]. 

An important factor in the progress of bioinformatics has been the constant increase in computer speed and memory capacity of desktop computers and the increasing sophistication of data processing techniques. The computation power of common personal computers has increased within 12 years approximately 100-fold in processor speed, 250-fold in RAM memory space and 500-fold or more in hard disk space, while the price has nearly halved. This enables acquisition, transformation, visuahsation and interpretation of large amounts of data at a fraction of the cost compared to 12 years ago. Presently, bioanalytical databases are also growing quickly in size and many databases are directly accessible via the Internet One of the first chemical databases to be placed on the Internet was the Brookha-ven protein data bank, which contains very valuable three-dimensional structural data of proteins. The primary resource for proteomics is the ExPASy (Expert Protein Analysis System) database, which is dedicated to the analysis of protein sequences and structures and contains a rapidly growing index of 2D-gel electrophoresis maps. Some primary biomolecular database resources compiled from spectroscopic data are given in Tab. 14.1. 

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