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PubMed2002

SCOP database in 2002: refinements accommodate structural genomics.

The SCOP (Structural Classification of Proteins) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are grouped into species and hierarchically classified into families, superfamilies, folds and classes. Recently, we introduced a new set of features with the aim of standardizing access to the database, and providing a solid basis to manage the increasing number of experimental structures expected from structural genomics projects. These features include: a new set of identifiers, which uniquely identify each entry in the hierarchy; a compact representation of protein domain classification; a new set of parseable files, which fully describe all domains in SCOP and the hierarchy itself. These new features are reflected in the ASTRAL compendium. The SCOP search engine has also been updated, and a set of links to external resources added at the level of domain entries. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.

Animals↗

PubMed2003

MMDB: Entrez's 3D-structure database.

Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. To this end, Entrez's search engine provides several powerful features: (i) links between databases, for example between a protein's sequence and structure; (ii) pre-computed sequence and structure neighbors; and (iii) structure and sequence/structure alignment visualization. Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative analysis. MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html.

Animals↗

PubMed2003

SSEP: Secondary structural elements of proteins.

SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein chains from 1670 protein structures and 6182 protein chains from 5425 protein structures in 25 and 90% non-redundant protein chains, respectively. The current version provides information about the alpha-helical segments and beta-strand fragments of varying lengths. In addition, it also contains the information about 3(10)-helix, beta- and nu-turns and hairpin loops. The free graphics program RASMOL has been interfaced with the search engine to visualize the three-dimensional structures of the user queried secondary structural fragment. The database is updated regularly and is available through Bioinformatics web server at http://cluster.physics.iisc.ernet.in/ssep/ or http://144.16.71.148/ssep/.

Databases, Protein↗

PubMed2003

Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors.

One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived through data mining of training sets of residues taken from the transmembrane-spanning segments of polytopic proteins. These residues correspond to short regions in which there is a deviation from the regular alpha-helical character (i.e. pi-helices, 3(10)-helices and kinks). A 'search engine' derived from these motif descriptors correctly identifies, and discriminates amongst instances of the above 'non-canonical' helical motifs contained in the SwissProt/TrEMBL database of protein primary structures. Our results suggest that deviations from alpha-helicity are encoded locally in sequence patterns only about 7-9 residues long and can be determined in silico directly from the amino acid sequence. Delineation of such variations in helical habit is critical to understanding the complex structure-function relationships of polytopic proteins and for drug discovery. The success of our current methodology foretells development of similar prediction tools capable of identifying other structural motifs from sequence alone. The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html.

Amino Acid Sequence↗

PubMed2004

Genew: the Human Gene Nomenclature Database, 2004 updates.

Genew, the Human Gene Nomenclature Database http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl is the only resource that provides data for all human genes that have approved symbols. It is managed by the HUGO Gene Nomenclature Committee (HGNC) as a confidential database, containing over 22 000 records, 75% of which are represented online by a publicly searchable text file. Since 2002, there have been significant improvements to the Genew search engine. Additionally we have increased our capacity to analyse confidential sequence data, which has enabled us to manage the large numbers of gene symbol requests that we receive from the chromosome sequencing consortia.

Animals↗

PubMed2004

SCOR: Structural Classification of RNA, version 2.0.

SCOR, the Structural Classification of RNA (http://scor.lbl.gov), is a database designed to provide a comprehensive perspective and understanding of RNA motif three-dimensional structure, function, tertiary interactions and their relationships. SCOR 2.0 represents a major expansion and introduces a new classification organization. The new version represents the classification as a Directed Acyclic Graph (DAG), which allows a classification node to have multiple parents, in contrast to the strictly hierarchical classification used in SCOR 1.2. SCOR 2.0 supports three types of query terms in the updated search engine: PDB or NDB identifier, nucleotide sequence and keyword. We also provide parseable XML files for all information. This new release contains 511 RNA entries from the PDB as of 15 May 2003. A total of 5880 secondary structural elements are classified: 2104 hairpin loops and 3776 internal loops. RNA motifs reported in the literature, such as 'Kink turn' and 'GNRA loops', are now incorporated into the structural classification along with definitions and descriptions.

Animals↗

PubMed2004

ProteinDBS: a real-time retrieval system for protein structure comparison.

We have developed a web server (ProteinDBS) for the life science community to search for similar protein tertiary structures in real time. This system applies computer visualization techniques to extract the predominant visual patterns encoded in two-dimensional distance matrices generated from the three-dimensional coordinates of protein chains. When meaningful contents, represented in a multi-dimensional feature space, have been extracted from distance matrices, an advanced indexing structure, Entropy Balanced Statistical (EBS) k-d tree, is utilized to index the data. Our system is able to return search results in ranked order from a database with 46 075 chains in seconds, exhibiting a reasonably high degree of precision. To our knowledge, this is the first real-time search engine for protein structure comparison. ProteinDBS provides two types of query method: query by Protein Data Bank protein chain ID and by new structures uploaded by users. The system is hosted at http://ProteinDBS.rnet.missouri.edu.

Computer Graphics↗

PubMed2005

IPD--the Immuno Polymorphism Database.

The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute.

Animals↗

PubMed2005

MITOMAP: a human mitochondrial genome database--2004 update.

MITOMAP (http://www.MITOMAP.org), a database for the human mitochondrial genome, has grown rapidly in data content over the past several years as interest in the role of mitochondrial DNA (mtDNA) variation in human origins, forensics, degenerative diseases, cancer and aging has increased dramatically. To accommodate this information explosion, MITOMAP has implemented a new relational database and an improved search engine, and all programs have been rewritten. System administrative changes have been made to improve security and efficiency, and to make MITOMAP compatible with a new automatic mtDNA sequence analyzer known as Mitomaster.

DNA, Mitochondrial↗

PubMed2006

Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.

Small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs) are named for their subcellular localization within nucleoli and Cajal bodies (conserved subnuclear organelles present in the nucleoplasm), respectively. They have been found to play important roles in rRNA, tRNA, snRNAs, and even mRNA modification and processing. All snoRNAs fall in two categories, box C/D snoRNAs and box H/ACA snoRNAs, according to their distinct sequence and secondary structure features. Box C/D snoRNAs and box H/ACA snoRNAs mainly function in guiding 2'-O-ribose methylation and pseudouridilation, respectively. ScaRNAs possess both box C/D snoRNA and box H/ACA snoRNA sequence motif features, but guide snRNA modifications that are transcribed by RNA polymerase II. Here we present a Web-based sno/scaRNA database, called sno/scaRNAbase, to facilitate the sno/scaRNA research in terms of providing a more comprehensive knowledge base. Covering 1979 records derived from 85 organisms for the first time, sno/scaRNAbase is not only dedicated to filling gaps between existing organism-specific sno/scaRNA databases that are focused on different sno/scaRNA aspects, but also provides sno/scaRNA scientists with an opportunity to adopt a unified nomenclature for sno/scaRNAs. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase provides an easy-to-use gateway to important sno/scaRNA features such as sequence motifs, possible functions, homologues, secondary structures, genomics organization, sno/scaRNA gene's chromosome location, and more. Approximate searches, in addition to accurate and straightforward searches, make the database search more flexible. A BLAST search engine is implemented to enable blast of query sequences against all sno/scaRNAbase sequences. Thus our sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research. The database is free available at http://gene.fudan.sh.cn/snoRNAbase.nsf.

Base Sequence↗

PubMed2006

MMDB: annotating protein sequences with Entrez's 3D-structure database.

Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's 'Related Structure' links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The 'Related Structure' service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure).

Databases, Protein↗

PubMed2003

Hypothenar hammer syndrome: a discrete syndrome to be distinguished from hand-arm vibration syndrome.

BACKGROUND: Hypothenar hammer syndrome (HHS) is a cause of vascular insufficiency to the hand and may be manifest as Raynaud's phenomenon. The cause is trauma to the vulnerable portion of the ulnar artery as it passes over the hamate bone, which may result in thrombosis, irregularity or aneurysm formation. AIM: This review was undertaken in order to clarify the features of HHS that may differentiate it from hand-arm vibration syndrome. METHODS: A tiered review of world literature was undertaken using Medline and EMBase as the primary search engines. Fifty-two relevant articles were critically reviewed. CONCLUSION: Colour and temperature changes occur more diffusely in HHS than in classical Raynaud's phenomenon and the absence of the triphasic colour change may alert clinicians to the diagnosis, which may be confirmed by Allen's test. Doppler or arteriographic studies are required for confirmation. It is important to recognize the possibility of HHS in the occupational setting as a potentially curable cause of Raynaud's phenomenon, distinct from hand-arm vibration syndrome. The possibility exists of HHS occurring as a result of repeated hypothenar trauma from vibrating tools, in which case the nature and magnitude of the individual episode of trauma may be more important than the weighted acceleration level of vibration exposure.

Arm Injuries↗

PubMed2003

Thoracic outlet syndrome--aspects of diagnosis in the differential diagnosis of hand-arm vibration syndrome.

BACKGROUND: Thoracic outlet syndrome (TOS) is a cause of vascular and neurological compromise to the arm and hand, and may manifest as Raynaud's phenomenon. It may be under-diagnosed. AIM: This review was undertaken in order to clarify the diagnostic and investigative features of TOS that may differentiate it from hand-arm vibration syndrome. METHODS: A tiered review of the world literature was undertaken using Medline and Embase as the primary search engines. CONCLUSION: Thoracic outlet syndrome most commonly presents with neurological symptoms in the arm. Vascular symptoms, including Raynaud's phenomenon, may occur in approximately 10% of cases. Careful clinical assessment by history and examination may reveal the elements of forearm and upper arm symptoms with postural exacerbation, which distinguish this condition from hand-arm vibration syndrome. The usefulness of investigation is unclear, but Doppler and neuroelectric studies may be valuable. Magnetic resonance imaging scan is the investigation of choice.

Arm↗

PubMed2005

Evidence-based decision making in an endoscopy nurse with respiratory symptoms exposed to the new ortho-phthalaldehyde (OPA) disinfectant.

BACKGROUND: ortho-Phthalaldehyde (OPA) can cause mucous irritation, respiratory symptoms and IgE-mediated hypersensitivity reactions. Very little information is available about OPA-related effects in health personnel. AIM: To report the decision-making process for the case of an endoscopy nurse complaining of cough and burning of the nose and throat during OPA exposure at work. METHODS: The problem focused on the relationship between OPA exposure and the respiratory symptoms and was investigated using an evidence-based (EB) medicine paradigm. RESULTS: A literature search was performed using the database Medline and the search engine Google. Papers and guidelines were assessed for their suitability in the EB case identification of suspected occupational asthma (OA). A multistep approach suggested by a guideline was considered most appropriate for practical use. The nurse shared the decision-making process and underwent evaluation of the clinical suspicion index and interventions for diagnosis of OA. Despite the high clinical suspicion index, the diagnosis of OA was excluded and any work restriction was avoided. Health surveillance follow-up showed a good clinical outcome and prompt recovery from respiratory symptoms after improvement of environmental control measures. CONCLUSION: The case study shows that the implementation of EB guidelines provides the occupational physician with an appropriate decision-making process for the identification and management of workers with suspected OA. Screening out of OA is highly relevant because diagnosis of disease requires removal from exposure and frequently impacts negatively on worker employment.

Adult↗

PubMed2002

Oximes in acute organophosphorus pesticide poisoning: a systematic review of clinical trials.

BACKGROUND: Acute organophosphorus (OP) pesticide poisoning is widespread in the developing world. Standard treatment involves the administration of intravenous atropine and an oxime to counter acetylcholinesterase inhibition at the synapse, but the usefulness of oximes is uncertain. AIM: To assess the evidence on the use of oximes in OP poisoning. DESIGN: Systematic review. METHODS: We searched Medline, Embase, and Cochrane databases (last check 01/02/02) for 'organophosphate' or 'oxime' together with 'poisoning' or 'overdose'. We cross-referenced from other articles, and contacted experts to identify unpublished studies. A Web search engine [www.google.com] was also used, with the keywords 'organophosphate', 'oxime', and 'trial' (last check 01/02/02). RESULTS: We found two randomized controlled trials (RCTs) involving 182 patients treated with pralidoxime. The RCTs found no benefit with pralidoxime, and have been used to argue that pralidoxime should not be used in OP poisoning. DISCUSSION: The RCT authors must be congratulated for attempting important studies in a difficult environment. However, their studies did not take into account recently clarified issues regarding outcome, and their methodology is unclear. A generalized statement that pralidoxime should not be used in OP poisoning is not supported by the published results. Oximes may well be irrelevant in the overwhelming self-poisoning typical of the tropics, but a large RCT comparing the current WHO-recommended pralidoxime regimen (>30 mg/kg bolus followed by >8 mg/kg/h infusion) with placebo is needed for a definitive answer. Such a study should be designed to identify any patient subgroups that might benefit from oximes.

Acute Disease↗

PubMed1998

An insight into rheumatology resources available on the World Wide Web.

The aim of this study was to gain an overview of rheumatology resources on the World Wide Web (WWW). A list of websites was generated using a commercial search engine and 'rheumatology' as a key word. A total of 154 websites were then evaluated with respect to origin and likely target audience; 43% of this initial group were either not accessible, repeats, or in a language other than English. Of the 87 websites we were able to analyse, we found that 67% originated from medical organizations and 51% were interpreted to be directed specifically at rheumatologists. Only 16% of websites were directed at patients only. The remainder were felt to contain information useful to both groups. Over half the websites felt to be of interest to patients contained advertisements. Although there is a lot of information relating to rheumatology on the WWW, it was invariably time consuming to access and there was little directed solely at patient education.

Advertising↗

PubMed2003

Nonprescription treatments of snoring or obstructive sleep apnea: an evaluation of products with limited scientific evidence.

PURPOSE: To evaluate the level of evidence regarding the safety and efficacy of nonprescription therapies used to treat snoring and obstructive sleep apnea, and form a consensus statement based on available data. REVIEWERS: Members of the American Academy of Sleep Medicine's Clinical Practice Review Committee. METHODS: A search of PubMed database using MeSH terms snore, apnea, and obstructive sleep apnea in August, 2002, including only articles published in English between 1990 and 2002 and of the World Wide Web, using Google search engine and the key words snoring and obstructive sleep apnea. Letters were sent to manufacturers of lubricant oral and nasal products requesting copies of scientific studies to support their claims. RESULTS AND CONCLUSIONS: Given the paucity and quality of scientific literature regarding the nonpharmacologic treatment of snoring and obstructive sleep apnea, members of the Clinical Practice Review Committee had insufficient information to develop standards of practice recommendations. Nevertheless, substantial publicity regarding such treatments is available to the general public. Very limited data are available to support a beneficial effect of these devices on snoring and minimal evidence is available to support their use in treating obstructive sleep apnea. Studies are limited by small numbers of participants and, in some instances, inadequate design, lack of statistical analysis, and sparse use of objective measurements. Many studies do not evaluate product safety, especially over extended use. Physicians may find this information useful in counseling their patients.

Consumer Product Safety↗

PubMed2002

Evaluation of plastic surgery information on the Internet.

The Internet allows vast access to medical information. Unlike most plastic surgery literature, the Internet is a quagmire of unfiltered information, not subject to peer review. To assess the accuracy of medical information on the Internet the authors studied one commonly performed elective procedure, classifying and defining the information retrieved. Using the keyword "breast augmentation," the authors compiled a list of the first 300 web sites, obtained from six distinct search engines, yielding 215 unique sites. They devised an instrument to evaluate each site for its accessibility, relevance, and accuracy. Of the 215 unique web sites evaluated, 20 were inaccessible, 24 were irrelevant, and 41 contained no medical information. Of the remaining 130 sites, almost 34% contained false or misleading information. Errors pertained most often to the technical details of the operation, potential benefits, and risks. In addition, exaggerated claims concerning alternative breast enhancement regimens, adverse sequelae of silicone breast implants, and potential effects on lactation were also seen commonly. A considerable amount of information regarding breast augmentation on the Internet was either misleading or inaccurate. Physicians can assist their patients with specific guidelines to allow them to process information discerningly, thereby diminishing the likelihood that medical decisions are based on misinformation.

Health Education↗