StreptomeDB: a resource for natural compounds isolated from Streptomyces species.

Bacteria from the genus Streptomyces are very important for the production of natural bioactive compounds such as antibiotic, antitumour or immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria. An enormous quantity of crucial data related to this genus has been generated and published, but so far no freely available and comprehensive database exists. Here, we present StreptomeDB (http://www.pharmaceutical-bioinformatics.de/streptomedb/). To the best of our knowledge, this is the largest database of natural products isolated from Streptomyces. It contains >2400 unique and diverse compounds from >1900 different Streptomyces strains and substrains. In addition to names and molecular structures of the compounds, information about source organisms, references, biological role, activities and synthesis routes (e.g. polyketide synthase derived and non-ribosomal peptides derived) is included. Data can be accessed through queries on compound names, chemical structures or organisms. Extraction from the literature was performed through automatic text mining of thousands of articles from PubMed, followed by manual curation. All annotated compound structures can be downloaded from the website and applied for in silico screenings for identifying new active molecules with undiscovered properties.

Mining and evaluation of molecular relationships in literature.

MOTIVATION: Specific information on newly discovered proteins is often difficult to find in literature. Particularly if only sequences and no common names of proteins or genes are available, preceding sequence similarity searches can be crucial for the process of information collection. In drug research, it is important to know whether a small molecule targets only one specific protein or whether similar or homologous proteins are also influenced that may account for possible side effects. RESULTS: prolific (protein-literature investigation for interacting compounds) provides a one-step solution to investigate available information on given protein names, sequences, similar proteins or sequences on the gene level. Co-occurrences of UniProtKB/Swiss-Prot proteins and PubChem compounds in all PubMed abstracts are retrievable. Concise 'heat-maps' and tables display frequencies of co-occurrences. They provide links to processed literature with highlighted found protein and compound synonyms. Evaluation with manually curated drug-protein relationships showed that up to 69% could be discovered by automatic text-processing. Examples are presented to demonstrate the capabilities of prolific. AVAILABILITY: The web-application is available at http://prolific.pharmaceutical-bioinformatics.de and a web service at http://www.pharmaceutical-bioinformatics.de/prolific/soap/prolific.wsdl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Compounds In Literature (CIL): screening for compounds and relatives in PubMed.

SUMMARY: Searching for certain compounds in literature can be an elaborate task, with many compounds having several different synonyms. Often, only the structure is known but not its name. Furthermore, rarely investigated compounds may not be described in the available literature at all. In such cases, preceding searches for described similar compounds facilitate literature mining. Highlighted names of proteins in selected texts may further accelerate the time-consuming process of literary research. Compounds In Literature (CIL) provides a web interface to automatically find names, structures, and similar structures in over 28 million compounds of PubChem and more than 18 million citations provided by the PubMed service. CIL's pre-calculated database contains more than 56 million parent compound-abstract relations. Found compounds, relatives and abstracts are related to proteins in a concise 'heat map'-like overview. Compounds and proteins are highlighted in their respective abstracts, and are provided with links to PubChem and UniProt. AVAILABILITY: An easy-to-use web interface with detailed descriptions, help and statistics is available from http://cil.pharmaceutical-bioinformatics.de. CONTACT: stefan.guenther@pharmazie.uni-freiburg.de.

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

Much of the information on the Cytochrome P450 enzymes (CYPs) is spread across literature and the internet. Aggregating knowledge about CYPs into one database makes the search more efficient. Text mining on 57 CYPs and drugs led to a mass of papers, which were screened manually for facts about metabolism, SNPs and their effects on drug degradation. Information was put into a database, which enables the user not only to look up a particular CYP and all metabolized drugs, but also to check tolerability of drug-cocktails and to find alternative combinations, to use metabolic pathways more efficiently. The SuperCYP database contains 1170 drugs with more than 3800 interactions including references. Approximately 2000 SNPs and mutations are listed and ordered according to their effect on expression and/or activity. SuperCYP (http://bioinformatics.charite.de/supercyp) is a comprehensive resource focused on CYPs and drug metabolism. Homology-modeled structures of the CYPs can be downloaded in PDB format and related drugs are available as MOL-files. Within the resource, CYPs can be aligned with each other, drug-cocktails can be 'mixed', SNPs, protein point mutations, and their effects can be viewed and corresponding PubMed IDs are given. SuperCYP is meant to be a platform and a starting point for scientists and health professionals for furthering their research.

SuperTarget and Matador: resources for exploring drug-target relationships.

The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of medical articles or textbooks. Therefore, we developed a one-stop data warehouse, SuperTarget that integrates drug-related information about medical indication areas, adverse drug effects, drug metabolization, pathways and Gene Ontology terms of the target proteins. An easy-to-use query interface enables the user to pose complex queries, for example to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target the same protein but are metabolized by different enzymes. Furthermore, we provide tools for 2D drug screening and sequence comparison of the targets. The database contains more than 2500 target proteins, which are annotated with about 7300 relations to 1500 drugs; the vast majority of entries have pointers to the respective literature source. A subset of these drugs has been annotated with additional binding information and indirect interactions and is available as a separate resource called Matador. SuperTarget and Matador are available at http://insilico.charite.de/supertarget and http://matador.embl.de.

Successful strategy to improve the specificity of electronic statin-drug interaction alerts.

PURPOSE: A considerable weakness of current clinical decision support systems managing drug-drug interactions (DDI) is the high incidence of inappropriate alerts. Because DDI-induced, dose-dependent adverse events can be prevented by dosage adjustment, corresponding DDI alerts should only be issued if dosages exceed safe limits. We have designed a logical framework for a DDI alert-system that considers prescribed dosage and retrospectively evaluates the impact on the frequency of statin-drug interaction alerts. METHODS: Upper statin dose limits were extracted from the drug label (SPC) (20 statin-drug combinations) or clinical trials specifying the extent of the pharmacokinetic interaction (43 statin-drug combinations). We retrospectively assessed electronic DDI alerts and compared the number of standard alerts to alerts that took dosage into account. RESULTS: From among 2457 electronic prescriptions, we identified 73 high-risk statin-drug pairs. Of these, SPC dosage information classified 19 warnings as inappropriate. Data from pharmacokinetic trials took quantitative dosage information more often into consideration and classified 40 warnings as inappropriate. This is a significant reduction in the number of alerts by 55% compared to SPC-based information (26%; p < 0.001). CONCLUSION: This retrospective study of pharmacokinetic statin interactions demonstrates that more than half of the DDI alerts that presented in a clinical decision support system were inappropriate if DDI-specific upper dose limits are not considered.

Ontology mapping for semantically enabled applications.

In this review, we provide a summary of recent progress in ontology mapping (OM) at a crucial time when biomedical research is under a deluge of an increasing amount and variety of data. This is particularly important for realising the full potential of semantically enabled or enriched applications and for meaningful insights, such as drug discovery, using machine-learning technologies. We discuss challenges and solutions for better ontology mappings, as well as how to select ontologies before their application. In addition, we describe tools and algorithms for ontology mapping, including evaluation of tool capability and quality of mappings. Finally, we outline the requirements for an ontology mapping service (OMS) and the progress being made towards implementation of such sustainable services.

Representation of target-bound drugs by computed conformers: implications for conformational libraries.

BACKGROUND: The increasing number of known protein structures provides valuable information about pharmaceutical targets. Drug binding sites are identifiable and suitable lead compounds can be proposed. The flexibility of ligands is a critical point for the selection of potential drugs. Since computed 3D structures of millions of compounds are available, the knowledge of their binding conformations would be a great benefit for the development of efficient screening methods. RESULTS: Integration of two public databases allowed superposition of conformers for 193 approved drugs with 5507 crystallised target-bound counterparts. The generation of 9600 drug conformers using an atomic force field was carried out to obtain an optimal coverage of the conformational space. Bioactive conformations are best described by a conformational ensemble: half of all drugs exhibit multiple active states, distributed over the entire range of the reachable energy and conformational space.A number of up to 100 conformers per drug enabled us to reproduce the bound states within a similarity threshold of 1.0 angstroms in 70% of all cases. This fraction rises to about 90% for smaller or average sized drugs. CONCLUSION: Single drugs adopt multiple bioactive conformations if they interact with different target proteins. Due to the structural diversity of binding sites they adopt conformations that are distributed over a broad conformational space and wide energy range. Since the majority of drugs is well represented by a predefined low number of conformers (up to 100) this procedure is a valuable method to compare compounds by three-dimensional features or for fast similarity searches starting with pharmacophores. The underlying 9600 generated drug conformers are downloadable from the Super Drug Web site 1. All superpositions are visualised at the same source. Additional conformers (110,000) of 2400 classified WHO-drugs are also available.

Misspellings in drug information system queries: characteristics of drug name spelling errors and strategies for their prevention.

INTRODUCTION: Efficient search for and finding drugs is essential for electronic drug information systems which, for their part, are prerequisites for computerized physician order entry systems and clinical decision support with the potential to prevent medication errors. Search failures would be critical: they may delay or even prohibit prescription processes or timely retrieval of vital drug information. We analyzed spelling-correction and error characteristics in drug searches and the suitability of auto-completion as prevention strategy. METHODS: A blank entry field was presented to the user for unbiased queries in a web-based drug information system containing >105,000 brand names and active ingredients accessible from all 5500 computers of the Heidelberg University Hospital. The system was equipped with an error-tolerant search. Misspelled but found drug names confirmed by users were aligned by dynamic programming algorithms, opposing misspelled and correct names letter by letter. We analyzed the ratios of correctly and incorrectly spelled but found drugs, frequencies of characters, and their position in misspelled search words. RESULTS: Without error-tolerant search, no results were found in 17.5% of all queries. Users confirmed 31% of all results found with phonetic error-correction support. Sixteen percent of all spelling errors were letters in close proximity to the correct letter on keyboards. On average, 7% of the initial letters in misspelled words contained errors. CONCLUSION: Drug information systems should be equipped with error-tolerant algorithms to reduce search failures. Drug initial letters are also error-prone, thus auto-completion is not a sufficient error-prevention strategy and needs additional support by error-tolerant algorithms.