Search Tools

Databo e-s and Data Sources in Chemi-stry 231 Table 5-2. Basic search tools of Boolean operators and truncation. 

Altschul S F, W Gish, W Miller, E W Myers and D J Lipman 1990. Basic Local Alignment Search Tool. Journal of Molecular Biology 215 403-410. 

The avaHabHity of citation searching tools is on the increase. A citation database for U.S. patents was first built by Search Check, Inc., which coHected aH U.S. patent citations back to their first appearance on patent copies in 1947. This database was subsequentiy made avaHable for on-line... 

SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman. Basic local alignment search tool. J Mol Biol 215 403-410, 1990. 

In addition to addressing the practicalities of database maintenance, we also aim to enhance the range of the facilities available, to make the information within CHIRBASE more readily accessible to users. CHIRBASE contains two form-based applications for query building designed to help novice or expert users to formulate queries the query menu and the automatic search tool. 

The aim of the fust dimension breadth is to reveal sequence-function relationships by comparing protein sequences by sequence similarity. Simple bioinformatic algorithms can be used to compare a pair of related proteins or for sequence similarity searches e.g., BLAST (Basic Local Alignment Search Tool). Improved algorithms allow multiple alignments of larger number of proteins and extraction of consensus sequence pattern and sequence profiles or structural templates, which can be related to some functions, see e.g., under http //www. expasy.ch/tools/ similarity. 

It is worth noting that the past few years have witnessed tremendous development of web-based information resources. Notably, the PubMed search tool [4] has made the investigation of any life sciences topic much easier. It offers keyword and author (as well as structure and sequence) searches and covers a wide range of medicinal chemistry-related journals. This resource, coupled with e-journals, affords the medicinal chemist the tools to keep up with any research topics of interest. Because of the public nature of the Web, now a chemist can sometimes find critical journal articles on the Web that do not show up until much later in traditional literature sources. It is not uncommon that scientific meeting presentations can be found on the Web. Indeed, the Internet tools we have all become familiar with also have made the professional life of the medicinal chemist much easier. 

ToxSeek is an NLM metasearch engine and clustering tool that enables the simultaneous searching of many different toxicology and environmental health information databases and web sites. This tool includes 59 databases including the TOXNET Search tool, as well as information sources from NLM, NIH, US Government, International and other sources. 

Bostrom, J. Reproducing the conformations of protein-bound ligands a critical evaluation of several popular conformational searching tools. /. Comput.-Aided Mol. Des. 2001, 35,1137-1152. 

ProteinProspector (http //prospector.ucsf.edu), database search tools, searching by peptide mass, with MS/MS or Edman data, etc. 

PubMed was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) at the National Institutes of Health (NIH). The PubMed database was developed in conjunction with publishers of biomedical literature as a search tool for accessing literature citations and linking to full-text journal articles at Web sites of participating publishers. Publishers that participate in PubMed supply NLM with their citations electronically prior to or at the time of publication. 

BLAST basic local alignment search tool... 

Sequence similarity searching Basic Local Alignment Search Tool (BLAST) http //www.ncbi.nlm.nih.gov/BLAST/ Comparison of novel sequences with known genes. 

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