Internet-based tools

MC Peitsch. PROMOD and SWISS-MODEL Internet-based tools for automated comparative protein modeling. Biochem Soc Trans 24 274-279, 1996. 

Peitsch MC. 1996. ProMod and Swiss-Model internet-based tools for automated comparative protein modeUing. Bio-chem Soc Trans 24(1) 274-279. 

Williams AJ (2008) Internet-based tools for communication and collaboration in chemistry. Drug Discov Today 13(ll-12) 502-506... 

A number of methods to predict physicochemical properties of compounds are available as public or commercial products. Table 9.1 lists some of the programs and their providers. Many programs have been developed for prediction of lipophilicity and aqueous solubility of chemicals. A more detailed overview of Internet-based tools that can be used for physicochemical property prediction can be also found elsewhere [142],... 

Peitsch M C 1996. Pro Mod and Swiss-Model- Internet-based Tools for Automated Comparative Protein Modelling. Biochemical Society Transactions 24-274-279... 

Further development should include using special database (e.g. online Internet based tool) that collects and analyses the accident and exposure data for the purpose of RSDI comparisons between countries. This database should be regularly maintained to ensure the accuracy of data and the RSDI indicators. The Globesafe database in Sweden could be one example in this regard. 

Underlying this modem model is an infrastmcture known as the World Wide Web, and this review will focus on how this paradigm differs from earlier ones, and how the standards and methods for expressing and utilizing chemical content in this medium have evolved during the period 1994-1997, and have been incorporated into a new generation of chemistry tools The specifically technical aspects of the operation of the Internet have been covered elsewhere, or in articles in other encyclopedias. Here we will focus on providing a brief overview of the chemical history of the Internet, followed by some specific illustrated examples of Internet-based tools and their applications, and conclude with some personal views on how the medium is likely to evolve. 

The rather abstract concepts discussed above, and also their limitations, are best illustrated by dissecting in detail how two simple Web-based computational chemistry tools can be constructed. The first will illustrate how a molecule can be selected from a database, visualized, and if desired used to initiate further database queries. The second example will show how infrared data presented in the form of a spectrum can be linked to theoretically computed normal vibrational modes as part of an animated model. The concepts illustrated here were originally described by us as hyperactive chemistry . No attempt here is made to explain every detail of the syntax employed in these examples, but rather to illustrate the basic concepts behind these tools. It is probable in any event that the syntax may change in the future, and these models should be taken as a snapshot of the state of Internet-based tools in early 1997 rather than as definitive examples. 

EPA has developed an evaluation tool, the PBT Profiler, which predicts PBT potential of chemicals. The PBT Profiler estimates environmental persistence (P), bioconcentration potential (B), and aquatic toxicity (T) of discrete chemicals based on their molecular structure. It is Internet-based and there is no cost for use. 

New pathogens can be identified and treatment regimes can change at any time. Therefore, it is more important for practitioners to focus on how to use tools to access the most up-to-date recommendations than on specific current prevention and treatment protocols. These tools are Internet-based and generally available free of charge to practitioners. 

To facilitate the searches of multiple Internet sources, metasearching is useful. Metasearch tools launch a single query across a set of Web-based health sites. One query returns a merged and often ranked list of hits, allowing the user to search several databases at once. Table 3-3 describes the specifics of new metasearch engines available to search for Internet-based health information. 

Use the computer-based tools that accompany the course. This textbook is accompanied by an Internet site that supplements the text. If you have access to it, you will find it useful at this stage in your studying. 

Links. PDB s search engine, the Structme Explorer, can be used to retrieve PDB records, as shown in Figure 5.2. The Structure Explorer is also the primary database of links to third-party aimotation of PDB structure data. There are a number of links maintained in the Structure Explorer to Internet-based three-dimensional structure services on other Web sites. Figme 5.2 shows the Structure Summary for the protein bamase (IBNR Bycroft et al., 1991). The Structure Explorer also provides links to special project databases maintained by researchers interested in related topics, such as structural evolution (FSSP Holm and Sander, 1993), structure-structure similarity (DALI Holm and Sander, 1996), and protein motions (Gerstein et al., 1994). Links to visualization tool-ready versions of the structure are provided, as well as authored two-dimensional images that can be very helpful to see how to orient a three-dimensional structure for best viewing of certain features such as binding sites. 

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