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Orientation of the Ligand in the Target Site

Algorithm, matching the sphere centers (described above) with ligand centers (usually ligand atoms). The matching criterion is based on a comparison of intersphere and interatom distances. Exhaustive or selective searches can be done over the match matrix. Careful placement of the spheres is an important step in getting good-quality results. The second type of method selectively samples all of orientation and conformation space using search engines. For example, the Metropolis algorithm and simulated annealing are used in QXP, and the genetic algorithm has been implemented an Autodock (McMartin and Bohacek, 1997 Morris et al., 1998). These algorithms have been studied extensively for many applications. Their strengths and limitations are well understood.

What is evidencebased medicine

The reader was guided in assessing the published literature in response to a given clinical scenario, to find relevant clinical articles, to assess the validity and understand the results of the identified papers, and to improve their clinical practice. Aided by computers, massive databases, and powerful search engines, these guidelines and the evidence-based movement empowered a new generation of practitioner and have had a profound impact on how studies are conducted, reported, and summarized. The massive proliferation of randomized clinical trials, the increasing numbers of systematic reviews and evidence-based guidelines, and the emphasis on appropriate methods of assessing diagnosis and prognosis, have affected how we practice medicine.

Constructing a PPP database for human plasma and serum proteins

The 18 participating laboratories using MS MS or FT-ICR-MS submitted a total of 42 306 protein identifications using various search engines and databases to handle spectra and generate peptide sequence lists from the specimens analyzed. which identified peptides gave 100 sequence matches. This integration process resulted in 9504 proteins in the IPI v2.21 database identified with one or more peptides. From this point of view, the PPP database is conservative, counting homologous proteins and all isoforms of particular proteins (and their corresponding genes) just once, unless the sequences actually differentiated any additional matches. We included at this stage proteins identified by matches to one or more peptide sequences of high or lower confidence according to cutpoints utilized with the various search engines used by different MS MS instruments. Tab. 1 shows the details of the cutpoints or filters used by each investigator and the numbers of high and lower confidence protein...

Background And Definitions

Current computer developments must be considered within the context of the entire information marketplace. The information marketplace includes the collection of computers, communications, software, and services engaged in all business and personal transactions. Today's computers successfully support many applications such as spreadsheets and databases. However, the larger problem involves the exchange of information between computers. A lack of standardization of data forms at different sites and with different machines and software packages makes communication difficult. Some degree of standardization may occur as large companies try to impose their standards on the marketplace in order to achieve dominance. The development of tools to encode and decode information and transactions is necessary to take advantage of widespread information exchange. A current area of great interest and growth is information exchange via the Internet. Although the information available through the...

Alternative search algorithms for peptide and protein identification

Kapp et al. 11 report a unique analysis of alternative search algorithms. They used one raw file from the Pacific Northwest National Laboratory LCQ-MS MS data on serum depleted only of IgG published by Adkins et al. 41 , which served as a basis for the later FT-ICR-MS analyses for the PPP (Lab 28). The same spectra were subjected to analyses with MASCOT, SEQUEST (with and without PeptideProphet), Sonar, Spectrum Mill, and XlTandem by experts familiar with the use of each. Careful manual inspection was applied, as well, though it is always a challenge to understand what exactly were the criteria used in manual inspection. The paper provides a useful description and categorization of the features of each search engine into heuristic algorithms and probabilistic algorithms. The authors then present and compare their performance identifying peptides and proteins, benchmarking them based on a range of specified false-positive rates. In all, 600 peptides were identified, of which 355 were...

Independent analyses of raw spectra or peaklists

After the original data submission protocol had been established, built upon pep-tide sequences and protein identifications, three groups emerged as having capability for centralized, independent analyses that would bypass the peculiarities of the search engine software embedded in particular MS instruments and the criteria applied by individual investigators in establishing thresholds for high and lower confidence identifications or applying manual inspection of the spectra.

Sources of further information and advice

A compendium of protein fingerprints (groups of conserved motifs used to characterise a protein family) is available from PRINTS (http Current news articles on proteomics are available from http www.bioexchange.com news proteomics.cfm. BioCyc knowledge library (http biocyc.org ) is another database collection that describes genomes and metabolic pathways. Database search engines like BLAST (of National Centre for Biotechnology Information) and FASTA (of the European Bioinformatics Institute) are useful for assessing sequence similarity and for homology searching against nucleotide and protein databases. Specific search engines and tools for mining sequence databases in conjunction with mass spectrometry data are also available (e.g., ProteinProspector (http prospector.ucsf.edu ), and Mascot (http

What is a reasonable survival strategy

PubMed (http pubmed.gov) is a U.S. taxpayer-supported, web-based search engine for thousands of medical journals encompassing over 15 million indexed citations. PubMed offers two evidence-based databases to filter and narrow your search results Clinical Study Categories, which identifies high quality studies limited to specific categories of interest and Systematic Reviews, which filters your results to include only systematic reviews. National Guidelines Clearinghouse (http guidelines.gov) is a U.S. taxpayer-supported database of practice guidelines which allows the user to browse by disease, treatment, originating organization, or guidelines. A detailed search engine retrieves evidence-based guidelines by author, diagnosis, therapy, prevention, target population, or date of publication. Guidelines can be viewed side by side to compare recommendations from different sources.

How to Test Your Ability to Evaluate Psychological Tests

A number of Web sites offer surveys, questionnaires, and other tools that purport to be psychological tests. Almost any search engine will lead you to these sites upon entering the terms psychological tests or personality tests. Among the many offerings in these sites are a variety of instruments, such as IQ tests, EQ tests, and career tests, that may look like psychological tests and appeal to the layperson but have very little or no legitimate scientific bases. Some of these so-called tests are offered free of charge others involve payment of a (typically) modest fee of 5, 10, or 15. In many cases, the free instruments do not include the full results (or even any results), unless a fee is first paid. Often test takers are not informed about the required fee until after they have completed the test.

Methods of search

The databases of the Cochrane Skin Group, the Cochrane Library to issue 2, 2001, Medline and Embase between 1968 and July 2001 were searched for articles that were trials of therapy of skin disease, or dermatomyositis, or the relationship of dermatomyositis to malignancy. Both Embase and Medline were searched using the Ovid search engine at Nottingham University. The searches involved the following terms

Teleradiology Case Present and Future

Telemedicine can be defined in a broad sense as any medicine-related interaction between a user and a provider that is not done face-to-face. The provider can be either a human being or an intelligent entity such as a search engine, an interactive video demonstration program, or a rule-based inference engine. The communication channels do not have to be identical in both directions. For instance, the user can send image data to a provider via satellite, and the provider can respond with a diagnostic report by telephone. Among others, telemedicine covers the following important scenarios

Dr Eric W Deutsch

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anti-coagulated plasma and (3) created a publicly-available knowledge base www.ebi.ac.uk pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations (b) protein identifications from 18 MS MS datasets (c) independent analyses from raw MS-MS spectra (d) search engine performance, subproteome analyses, and biological insights (e) antibody arrays and (f) direct MS SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two...

Integration

Integration of e-technologies is the ability to harness different e-technological developments, including network infrastructure, relevant hardware and software, and Web interface design, into a single, flexible, and integrated platform for the delivery of a seamless continuum of care. The Web development language chosen must be both flexible and functional in different computing systems, Web browsers, and search engines. As indicated in earlier chapters, the use of XML to support interactive functions and secured transactions on the Internet is one approach to a common and convenient interface. Other technologies that might be harnessed and integrated include an information grid to organize the piecemeal information captured throughout the Internet, with a language translator facility to extract information captured in different languages, and effective document management systems to ensure fast and effective delivery of information to e-consumers.

Discussion

Citly including experimental analyses of plasma samples from the same people and animals whose liver and brain specimens are studied. Several of the challenges listed above which involve search engine performance and integration of peptide identifications and protein matches with different databases deserve systematic investigation. Furthermore, quantitative analyses of concentrations, interactions, and networks will be increasingly important and feasible 63 .

Internet

One may choose to limit the topic area and focus on a specific aspect of encapsulation, e.g. cyclodextrins. A search on cyclodextrins brings the number of hits down to 89,000 - still a bit unmanageable. But again one can browse the top 50-100 hits and get an overview of the broad activity in cyclodextrins or narrow the topic more by putting in qualifying key words. Simply tying cyclodextrins to 'flavor' brought the number down to 367. That is very manageable. It is worth noting that there are many search engines available and each offers unique search mechanisms criteria.

Animal models

As opposed to genetically driven screens such as targeting and trapping, pheno-typically driven screens allow a higher throughput of mutants, but without a molecular tag of the mutated genes (Cox and Brown, 2003). Mutations are usually chemically induced, e.g. by N-ethyl-N-nitrosourea (ENU), and banks of mutants are available for fly, zebrafish and mouse. The largest and most recent murine screens employ structured prenatal and postnatal programmes to assess the phenotypes. For instance, external appearance is scored, biochemical, radiological, haematological, immunological parameters assessed, and baseline cognitive and behavioural screens undertaken. Novel imaging techniques, such as MRI, offer the opportunity of a reasonably quick means of detecting internal malformations, such as cardiac defects (Schneider et al., 2003). The main centres conducting this work maintain search engines allowing identification of mutants that potentially model human disorders (e.g. http...

Going Online

What did we ever do before search engines A wealth of information on endometriosis is available on the Web, most of it available simply by typing endometriosis into your search engine. If you want to go to the latest research and physician studies, go to online medical sites. If you want to chat or join bulletin board groups, plenty of those are available too.

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