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At least 1,369 records · Page 76Linked to original sources
PubMed1997

HIV-1 integrase pharmacophore: discovery of inhibitors through three-dimensional database searching.

Starting from a known inhibitor of human immunodeficiency virus type 1 (HIV-1) integrase (IN); caffeic acid phenethyl ester (CAPE), a putative three-point pharmacophore for binding of inhibitors to IN was derived. This pharmacophore was used to search the National Cancer Institute three-dimensional (3D) structural database. Out of the open, nonproprietary part of this database, comprising approximately 200000 compounds, 267 structures were found to match the pharmacophore in at least one conformation, and 60 of those were tested in an in vitro assay against HIV-1 IN. Out of these, 19 were found to inhibit both the 3'-processing and strand transfer of IN at micromolar concentrations. In order to test the validity of this pharmacophore, a small 3D database of 152 published IN inhibitors was built. A search in this database yielded a statistically significant correlation of the presence of this pharmacophore and the potency of the compounds. An automated pharmacophore identification procedure performed on this set of compounds provided additional support for the importance of this pharmacophore for binding of inhibitors to IN and hinted at a possible second pharmacophore. The role of aromatic moieties in the binding of ligands to HIV-1 IN through interactions with divalent metal cations, which are known to be necessary for activity of the enzyme, was explored in ab initio calculations.

Caffeic Acids↗
PubMed2001

Database reusability in intelligent medical systems.

Reuse or reusability is not a specific, algorithmic, heuristic or only a simple set of guidelines. Database reuse means the use of an existing component--a database entity--in a new context, either elsewhere in the same system or in another system. According to different definitions, an intelligent system is a "power tool for thinking"; but on the other side it is only a kind of information system with built-in knowledge to support decisions made by human experts. Similar conclusions could be made for intelligent medical systems and introduce the database reusability in this environment with a purpose to increase the quality of an intelligent medical system. In the paper the problem of the database reusability will be presented more in detail, especially its integration in an intelligent medical system. Finally, the results of such integration and the benefits for the medicine will be discussed.

Artificial Intelligence↗
PubMed1997

Strategies for the determination of pharmacophoric 3D database queries.

Strategies are described for constructing pharmacophoric 3D database queries, based on a series of active and inactive analogs. The results are highly selective database queries, which are consistent with the generally accepted pharmacophore for a number of systems. The foundation of these strategies is the method of Mayer, Naylor, Motoc and Marshall [J. Comput.-Aided Mol. Design, 1 (1987) 3] for inferring a unique binding geometry for angiotensin-converting enzyme (ACE) inhibitors. The strategies described here generalize their approach to cases where the chemical features responsible for binding are not a priori apparent, and to cases where the binding geometry deduced by that method is not unique. The key new insight, the selectivity principle, is to rank the multiple solutions produced by the method of Mayer et al. by their selectivity, a value that is related to the proportion of a database that is returned as a database hit list. Retrospective analyses are described for D2-antagonists, ACE inhibitors, fibrinogen antagonists, and beta 2-antagonists.

Adrenergic beta-Antagonists↗
PubMed2000

Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors.

We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRID. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3D database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.

Benzamidines↗
PubMed2000

Assessing phytoestrogen exposure in epidemiologic studies: development of a database (United States).

BACKGROUND AND OBJECTIVE: Phytoestrogens (weak estrogens found in plants or derived from plant precursors by human metabolism) have been hypothesized to reduce the risk of a number of cancers. However, epidemiologic studies addressing this issue are hampered by the lack of a comprehensive phytoestrogen database for quantifying exposure. The purpose of this research was to develop such a database for use with food-frequency questionnaires in large epidemiologic studies. METHODS: The database is based on consumption patterns derived from semistructured interviews with 118 African-American, Latina, and white women residing in California's San Francisco Bay Area. HPLC-mass spectrometry was used to determine the content of seven specific phytoestrogenic compounds (i.e. the isoflavones: genistein, daidzein, biochanin A, and formononetin; the coumestan: coumestrol; and the plant lignans: matairesinol and secoisolariciresinol) in each of 112 food items/groups. RESULTS: Traditional soy-based foods were found to contain high levels of genistein and daidzein, as expected, as well as substantial amounts of coumestrol. A wide variety of "hidden" sources of soy (that is, soy protein isolate, soy concentrate, or soy flour added to foods) was observed. Several other foods (such as various types of sprouts and dried fruits, garbanzo beans, asparagus, garlic, and licorice) were also found to be substantial contributors of one or more of the phytoestrogens analyzed. CONCLUSIONS: Databases, such as the one described here, are important in assessing the relationship between phytoestrogen exposure and cancer risk in epidemiologic studies. Agencies, such as the United States Department of Agriculture (USDA), that routinely provide data on food composition, on which epidemiologic investigations into dietary health effects are based, should consider instituting programs for the analysis of phytochemicals, including the phytoestrogens.

Adult↗
PubMed2001

The study on the web-based Clinical Database Management System of Oriental Pulse Waveform.

There are many database-oriented sites on the web, which provide basic medical knowledge, hospital information, and medical counseling. However, there are only a few oriental pulse databases on the web. In this perspective, the goal of this study is to develop the Clinical Database Management System of Oriental Pulse Wave Form using the World Wide Web. Accordingly, this study has conducted researches in the Web-based diagnosis data management system of pulse waveform as well as the method of transmitting the data of pulse waveform. In order to set the standard for the documents of the pulse waveform of patients, the web-based clinical database management system has been developed.

Database Management Systems↗
PubMed1999

Using Department of Veterans Affairs Administrative databases to examine long-term care utilization for men and women veterans.

We examined long-term care (LTC) utilization by male and female veterans using administrative databases maintained by VA. Research questions included: (1) Which LTC services are utilized? (2) Do utilization patterns of older veterans differ from those of elderly persons in the general U.S. population? (3) Do LTC needs of veterans vary by gender? We were unable to track LTC utilization of individuals across administrative databases. Some databases could only provide information at the national level, or alternatively, were available only at local facilities, or only at the patient or program-level data--making it impossible to get a clear picture of all the services received by an individual. Those planning to use administrative databases to conduct research must: (1) take more time than expected; (2) be flexible/willing to compromise, (3) "ferret out" information, and (4) recognize that because of dynamism inherent in information systems, results may change over time.

Age Factors↗
PubMed2002

The cadherin superfamily database.

The cadherin superfamily is a large protein family with diverse structures and functions. Because of this diversity and the growing biological interest in cell adhesion and signaling processes, in which many members of the cadherin superfamily play a crucial role, it is becoming increasingly important to develop tools to manage, distribute and analyze sequences in this protein family. Current profile and motif databases classify protein sequences into a broad spectrum of protein superfamilies, however to provide a more specific functional annotation, the next step should include classification of subfamilies of these protein superfamilies. Here, we present a tool that classified greater than 90% of the proteins belonging to the cadherin superfamily found in the SWISS PROT database. Therefore, for most members of the cadherin superfamily, this tool can assist in adding more specific functional annotations than can be achieved with current profile and motif databases. Finally, the classification tool and the results of our analysis were integrated into a web-accessible database (http://calcium.uhnres. utoronto.ca/cadherin).

Amino Acid Motifs↗
PubMed2003

Fast 3D molecular superposition and similarity search in databases of flexible molecules.

We present a new method (fFLASH) for the virtual screening of compound databases that is based on explicit three-dimensional molecular superpositions. fFLASH takes the torsional flexibility of the database molecules fully into account, and can deal with an arbitrary number of conformation-dependent molecular features. The method utilizes a fragmentation-reassembly approach which allows for an efficient sampling of the conformational space. A fast clique-based pattern matching algorithm generates alignments of pairs of adjacent molecular fragments on the rigid query molecule that are subsequently reassembled to complete database molecules. Using conventional molecular features (hydrogen bond donors and acceptors, charges, and hydrophobic groups) we show that fFLASH is able to rapidly produce accurate alignments of medium-sized drug-like molecules. Experiments with a test database containing a diverse set of 1780 drug-like molecules (including all conformers) have shown that average query processing times of the order of 0.1 seconds per molecule can be achieved on a PC.

Algorithms↗
PubMed2003

Design and implementation of a common drug information database for a university hospital.

BACKGROUND: Providing high quality problem-oriented drug information relies on the ability to easily collect appropriate background information on clinical cases, to access relevant information from published sources by defined search strategies and to store and retrieve previously answered questions. To do this efficiently, an easy-to-use, flexible and reliable drug information database is necessary. METHODS: We designed and implemented an Intranet-based drug information database for a major university hospital in Germany. The overall design and the technical details of its design are discussed. We developed a generic, XML-based data model for pharmaceutical inquiries including a MeSH-oriented system of 99 pharmaceutical qualifiers to enable efficient indexing of questions and the searching of indexed questions. RESULTS: The system provides query statistics and various search algorithms. The software implementation takes into account recent FDA recommendations for software used in clinical trials; internal review for quality control is supported. The database currently consists of 4224 records after 3.5 years of operation. Each inquiry consists of 50 items, 18 of 50 are categorized; 135 text elements support data entry. Our evaluation is focused on technical feasibility, user acceptance and query patterns. CONCLUSION: The intensive use and widespread acceptance of the database indicates a need for a computerized drug information system and suggests that Intranet technology can perform this task.

Abstracting and Indexing↗
PubMed2000

Pharmacovigilance based on prescription databases.

Prescription databases are indispensible in drug safety research and surveillance. For suspected rare serious adverse drug reactions, the confirmation and quantitative risk assessment requires proper epidemiological studies. Often prescription databases provide the information on drug exposure for such studies. Aberrant drug utilization in terms of overuse, underuse, polypharmacy etc. may be a threat to the health of the patient, and these aspects can best be studied by prescription databases. In cases of international drug safety alerts, prescription databases may provide information required for rational actions to be taken.

Aged↗
PubMed1998

Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex.

Many important cell mechanisms are carried out and regulated by multi-protein complexes, for example, transcription and RNA processing machinery, receptor complexes and cytoskeletal structures. Most of these complexes remain only partially characterized due to the difficulty of conventional protein analysis methods. The rapid expansion of DNA sequence databases now provides whole or partial gene sequences of model organisms, and recent advances in protein microcharacterization via mass spectrometry allow the possibility of linking these DNA sequences to the proteins in functional complexes. This approach has been demonstrated in organisms whose genomes have been sequenced, such as budding yeast. Here we report the first characterization of an entire mammalian multi-protein complex using these methods. The machinery that removes introns from mRNA precursors--the spliceosome--is a large multi-protein complex. Approximately half of the components excised from a two-dimensional gel separation of the spliceosome were found in protein sequence databases. Using nanoelectrospray mass spectrometry, the remainder were identified and cloned using public expressed sequence tag (EST) databases. Existing EST databases are thus already sufficiently complete to allow rapid characterization of large mammalian protein complexes via mass spectrometry.

Amino Acid Sequence↗
PubMed2003

Comparison of nutrient intake data calculated on the basis of two different databases. Results and experiences from a Swedish-Finnish study.

BACKGROUND AND OBJECTIVE: In international surveys of food consumption and nutrient intake, it is essential that the dietary data are comparable when different databases and calculation programs are used. The aim of the present analysis was to examine the comparability of nutrient intake data calculated on the basis of the Swedish food composition database PC-kost and the Finnish food composition database Nutrica. SUBJECTS AND METHODS: A total of 20 male adults currently living in Sweden were selected from a group of Finnish twins of the Finnish Twin Cohort Study. Food consumption data were collected by means of diet history interviews. The estimated intakes of 30 nutrients calculated on the basis of PC-kost were compared to the corresponding estimates calculated on the basis of Nutrica. The calculation procedures were standardised. RESULTS: No statistically significant differences were observed in the mean intakes of energy, total fat, saturated fat, carbohydrates, dietary fibre, alcohol, cholesterol, vitamin A, retinol, beta-carotene, vitamin D, alpha-tocopherol, riboflavin, niacin, vitamin B(12), vitamin C or phosphorus. PC-kost yielded a 20% higher intake (NS) for vitamin D and 23% higher intake (P<0.001) for thiamine than Nutrica, which is mainly attributed to the differences in the enrichment of foodstuffs between Sweden and Finland. Conversely, PC-kost yielded 53% lower values (P<0.001) for selenium than Nutrica, owing to the increased selenium content in many Finnish foodstuffs as a result of the addition of selenium to fertilisers. Statistically significant differences were found for protein, monounsaturated fatty acids, vitamin B(6), iron and sodium (5-9% higher values from PC-kost) and for polyunsaturated fatty acids, folate, zinc, calcium, magnesium and potassium (4-10% lower values from PC-kost). The variation in the intake of these nutrients between the two methods may be explained by the differences in foodstuff-specific nutrient values (eg product formulations), or differences in the sources of data, recipes or calculation procedures. The correlation coefficient was > or =0.81 for most nutrients. At least 85% of the subjects in each PC-kost quintile were classified into the same or adjacent Nutrica quintile for all nutrients. CONCLUSIONS: Our results indicate that, for a dominant part of the examined nutrients, the estimated intakes calculated by means of standardised procedures using the PC-kost and Nutrica databases are comparable between Sweden and Finland. Differences observed for some nutrients reflect either actual differences in foods between the two countries or methodological differences in the assessment of nutrient intakes.

Aged↗
PubMed2000

Using the CATH domain database to assign structures and functions to the genome sequences.

The CATH database of protein structures contains approximately 18000 domains organized according to their (C)lass, (A)rchitecture, (T)opology and (H)omologous superfamily. Relationships between evolutionary related structures (homologues) within the database have been used to test the sensitivity of various sequence search methods in order to identify relatives in Genbank and other sequence databases. Subsequent application of the most sensitive and efficient algorithms, gapped blast and the profile based method, Position Specific Iterated Basic Local Alignment Tool (PSI-BLAST), could be used to assign structural data to between 22 and 36 % of microbial genomes in order to improve functional annotation and enhance understanding of biological mechanism. However, on a cautionary note, an analysis of functional conservation within fold groups and homologous superfamilies in the CATH database, revealed that whilst function was conserved in nearly 55% of enzyme families, function had diverged considerably, in some highly populated families. In these families, functional properties should be inherited far more cautiously and the probable effects of substitutions in key functional residues carefully assessed.

Algorithms↗
PubMed1998

Using biomedical databases in everyday clinical practice: the Front-Line Evidence-Based Medicine project in North Thames.

The aims of this project were to assess the feasibility of using biomedical databases in everyday clinical settings, and the infrastructure needed to support such practice. Fourteen firms or units whose lead clinician was enthusiastic for the principles of evidence-based medicine were provided with 24-h access to databases in their clinics or offices. All members of the firms were trained in the principles of evidence-based practice and in the use of databases for finding evidence. The firms were volunteers from a variety of specialties in both hospital and community Trusts in North Thames Region. Assessment of changes in practice was carried out by questionnaire and interview. Also, any changes needed to improve the use of primary research data in everyday clinical settings was investigated. Seven firms found that the project had made their journal clubs and their clinical discussion meetings more structured and focused, with research evidence for and against interventions discussed. The use of evidence in a case-related form was limited by the time available. The other seven firms were: dissatisfied with their training, dissatisfied with their computer facilities or lacked time. The changes necessary to improve the utilization of research data included: closer collaboration with librarians, continuing training and fast delivery of documents. The limitations of this study are that initial data were not recorded and the assessments made were subjective. Using biomedical databases in everyday clinical practice could be feasible provided that there is a coordinated implementation strategy, which requires a significant commitment of time and resources from all parties involved (clinicians, other health care professionals, librarians and managers).

Computer User Training↗
PubMed1996

Selecting a database for literature searches in nursing: MEDLINE or CINAHL?

This study compares the usefulness of the MEDLINE and CINAHL databases for students on post-registration nursing courses. We searched for nine topics, using title words only. Identical searches of the two databases retrieved 1162 references, of which 88% were in MEDLINE, 33% in CINAHL and 20% in both sources. The relevance of the references was assessed by student reviewers. The positive predictive value of CINAHL (70%) was higher than that of MEDLINE (54%), but MEDLINE produced more than twice as many relevant references as CINAHL. The sensitivity of MEDLINE was 85% (95% CI 82-88%), and that of CINAHL was 41% (95% CI 37-45%). To assess the ease of obtaining the references, we developed an index of accessibility, based on the holdings of a number of Irish and British libraries. Overall, 47% of relevant references were available in the students' own library, and 64% could be obtained within 48 hours. There was no difference between the two databases overall, but when two topics relating specifically to the organization of nursing were excluded, references found in MEDLINE were significantly more accessible. We recommend that MEDLINE should be regarded as the first choice of bibliographic database for any subject other than one related strictly to the organization of nursing.

Choice Behavior↗
PubMed2002

Evaluating DNA tests of motherless cases using a Philippine genetic database.

BACKGROUND: In 5 percent of paternity determination cases, only DNA samples from the alleged father and child pairs are tested. The absence of the mother's DNA increases the probability of false paternity inclusions, which affects laboratories that use a limited number of DNA markers. The effect of coincidental matches between unrelated individuals on DNA tests of motherless cases was determined using the Philippine population genetic database of the National Capital Region (NCR). STUDY DESIGN AND METHODS: Seven short tandem repeat (STR) markers were used, namely HUMvWA, HUMTH01, HUMCSF1PO, HUMFOLP23, D8S306, HUMFES/FPS, and HUMF13A01. Values of the probability of paternity with (W) and without a mother (W(-mother)) were determined using the equation W = cumulative likelihood ratio/cumulative likelihood ratio + 1). These values were determined for 50 volunteer families and compared with values calculated from randomly matched pairs in a reference NCR population database. RESULTS: The W and W(-mother) values of the 50 families range from 96.48 to 99.99 percent and 79.76 to 99.99 percent, respectively. In the NCR database, 195 coincidental matches in seven STR loci out of 5253 possible pairs (3.71%) were detected with W(-mother) values ranging from 12.47 to 99.83 percent. Of these, 53 and 10 random pairs have W(-mother) greater than 95.0 and 99.0 percent, respectively. CONCLUSION: W was higher than W(-mother) in the 50 families. However, the existence of unrelated individuals in the NCR database that randomly matched at seven STR loci and that has W(-mother) values greater than 99.0 percent highlights the need for greater precaution when dealing with motherless cases.

Databases, Genetic↗
PubMed2002

Software development, nomenclature schemes, and mapping strategies for an international pediatric cardiac surgery database system.

The field of congenital heart surgery has the opportunity to create the first comprehensive international database for a medical subspecialty. An understanding of the demographics of congenital heart disease and the rapid growth of computer technology leads to the realization that creating a comprehensive international database for pediatric cardiac surgery represents an important and achievable goal. The evolution of computer-based data analysis creates an opportunity to develop software to manage an international congenital heart surgery database and eventually become an electronic medical record. The same database data set for congenital heart surgery is now being used in Europe and North America. Additional work is under way to involve Africa, Asia, Australia, and South America. The almost simultaneous publication of the European Association for Cardio-thoracic Surgery/Society of Thoracic Surgeons coding system and the Association for European Paediatric Cardiology coding system resulted in the potential for multiple coding. Representatives of the Association for European Paediatric Cardiology, Society of Thoracic Surgeons, European Association for Cardio-thoracic Surgery, and European Congenital Heart Surgeons Foundation agree that these hierarchical systems are complementary and not competitive. An international committee will map the two systems. The ideal coding system will permit a diagnosis or procedure to be coded only one time with mapping allowing this code to be used for patient care, billing, practice management, teaching, research, and reporting to governmental agencies. The benefits of international data gathering and sharing are global, with the long-term goal of the continued upgrade in the quality of congenital heart surgery worldwide.

Cardiac Surgical Procedures↗