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VAST is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. Related structures for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search page also allows you to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors. Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one. From the MMDB Structure summary pages, retrieved via Entrez, structure neighbors are available for protein chains and individual structural domains. If you already know a PDB/MMDB-Id you can try this at once, using the input form in the right column. VAST Search is a service that allows searching for structural neighbors starting with a set of 3D-coordinates specified by the user. This service is meant to be used with newly determined protein structures that are not yet part of MMDB. Structure neighbors for proteins already in MMDB have been pre-computed and can simply be looked up from MMDB''s Structure summary pages!

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core performs research activities to create a wide array of industrial technologies using genomes and the other biological information to fulfill their mission. CBRC hosts research staff experts in diverse fields spanning computer science, mathematics, physics, chemistry, and biology and scientists affiliated with other institutions, with whom they work closely on joint, collaborative projects. Core offers internally developed and maintained software applications and databases, with corresponding external resources.

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• SciCrunch
• 16 years ago - by Anonymous

The Microbe Division in RIKEN-BRC has been collecting, preserving, and distributing cultured microbial strains as one of the leading culture collections in the world since established as Japan Collection of Microorganisms (JCM) in 1981. JCM aims to contribute to scientific communities by maintaining and serving high-quality microbial resources useful for general microbial studies and various research fields particularly in health and environmental science. JCM has participated in the National BioResource Project supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan as the core facility for General Microbes. JCM maintains approximately 19,900 strains as of Sept. 2010, and the approximate numbers of the available strains from JCM are: 7,400 strains of aerobic and anaerobic bacteria including actinomycetes, 300 strains of archaea, and 4,100 strains of fungi including yeasts (in total ca. 12,000 strains). Strains held at JCM are limited to those classified in Risk Group 1 or 2. Information of the available strains is opened to the public through the JCM On-line Catalogue Database. Genomic DNA samples of some strains are also distributed in cooperation with RIKEN BRC-DNA Bank. More than 3,500 strains are annually distributed to domestic and overseas researchers. JCM welcomes a deposit of microbial strains published or designed to be published in scientific papers as well as an order for microbial cultures.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

It is a prospective cohort study designed to investigate the relationship between sleep disordered breathing and cardiovascular disease. Participants were recruited from nine existing epidemiological studies in which data on cardiovascular risk factors had been collected previously.

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• SciCrunch
• 14 years ago - by Anonymous

The purpose of these three Banks (SUDDEN DEATH BRAIN AND TISSUE BANK, HIV BRAIN AND TISSUE BANK, and CJD BRAIN AND TISSUE BANK) is to collect donated samples from the brain and other organs of the body during post mortem examination, and to make these available for medical research. All the samples stored in the Edinburgh Banks are fully authorized for research by families and ethically approved for research use in accordance with the terms of current UK Human Tissue legislation. During the last 100 years or so, much of our knowledge of brain disorders has come from the study of post mortem tissues, based on identifying the differences between diseased and control (normal) brains. Advances in the diagnosis and treatment, as well as understanding the genetic background, of disorders such as Alzheimer''s disease, dementia with Lewy bodies, Parkinson''s disease and the effects of head injury have all depended on research using Brain Bank resources in different countries. Brain Banking in Edinburgh commenced in 1990, focusing specifically on HIV infection of the brain and on Creutzfeldt-Jakob disease (CJD). Significant progress in understanding these two brain infections has resulted both from the research in Edinburgh and from the work of scientists worldwide who have used tissue samples from the Edinburgh Brain Banks. These resources proved vital in establishing variant CJD as a new disease, different from the classic sporadic form and in demonstrating the brain changes in pre-AIDS and AIDS, particularly in drug abusers. In 2005 a third brain bank was established in Edinburgh with the specific aim of collecting donated normal brain tissue samples from the forensic post mortem service since there is a worldwide shortage of such material. This Bank also collects samples donated from individuals with psychiatric disorders or a history of head injury or of drug and alcohol addiction.

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• SciCrunch
• 16 years ago - by Anonymous

Free open-source software for exploring and analyzing large, high-dimensional image-derived data. It includes machine learning tools for identifying complex and subtle phenotypes. Source code and accompanying files are available. It is designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

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• SciCrunch
• 16 years ago - by Anonymous

A software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. This software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification is provided as a single executable. Crux is implemented in C and is distributed with source code freely to noncommercial users. Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification.

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• SciCrunch
• 16 years ago - by Anonymous

The intellectual system GenExpress designed for analysis of genomic regulatory sequences of higher eukaryotes comprises the following major units: (1) the database of transcription regulatory regions of eukaryotic genes TRRD that contains the description of regulatory regions of 427 eukaryotic genes, including 2133 transcription factor binding sites, 78 composite regulatory elements, 593 enhancers, and other types of transcription-regulating elements; (2) the database Activity that comprises the available data on the activity of the sites involved in the regulation of gene expression as well as the physico-chemical, conformational, and statistical DNA/RNA properties significant for the activity of these sites; (3) the database for gene networks GeneNet that contains the information on groups of the genes functioning coordinately to provide expression of genetic information; (4) a set of programs for detecting functional sites and predicting their activity; (5) programs for visualization of the information contained in the listed databases and the results of analysis; (6) semantic means to provide user''s navigation in the system. SRS (Sequence Retrieval System) query language was chosen for the system GenExpress, as it is widespread and Internet-compatible. GenExpress is available at /mgs/systems/geneexpress/. Applications of the system to analysis of the structure-function organization of human genomic nucleotide sequences are considered.

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• SciCrunch
• 16 years ago - by Anonymous

Databases which provide clustered sets of sequences from UniProt Knowledgebase and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences from view. The UniRef100 database combines identical sequences and sub-fragments with 11 or more residues (from any organism) into a single UniRef entry. The sequence of a representative protein, the accession numbers of all the merged entries, and links to the corresponding UniProtKB and UniParc records are all displayed in the entry. UniRef90 and UniRef50 are built by clustering UniRef100 sequences with 11 or more residues such that each cluster is composed of sequences that have at least 90% (UniRef90) or 50% (UniRef50) sequence identity to the longest sequence (UniRef seed sequence). All the sequences in each cluster are ranked to facilitate the selection of a representative sequence for the cluster.

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• SciCrunch
• 16 years ago - by Anonymous

Biomarker Commons aggregates news and research on disease biomarkers, and includes links to biomarker journals, resources and commercial services. There are a number of biomarkers in use today, not only in experimental research but in the clinical setting. * Translation biomarkers are used in both a preclinical (i.e. animal models) and clinical setting * Early detection biomarkers are used to identify the earliest stages of disease onset * Diagnostic biomarkers are used to identify the presence or absence of a specific disease state * Staging biomarkers are used to distinguish between different stages of a chronic disorder * Prognostic biomarkers are used to determine patient survival probability * Disease biomarkers are related to a clinical outcome or measure of disease * Predictive or efficacy biomarkers are used to predict the efficacy of a specific drug therapy * Target biomarkers are used to determine the interaction of a drug or small molecule with its target * Mechanism biomarkers are used to report on the downstream effects of a drug * Toxicity biomarkers are used to determine the toxicological effects of drugs on an in vitro or in vivo system * Surrogate biomarkers are regarded as valid substitutes for measuring clinical outcomes Users may search biomarker news (search by tags, news archive. or insights), sign up for biomarker news email alerts, follow biomarker commons and view biomarker news top tags

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• SciCrunch
• 16 years ago - by Anonymous

A relational database with dynamic querying and data integration that can be used by researchers to identify genetic sequences with a high probability of being associated with aflatoxin accumulation resistance, according to multiple lines of evidence. CFRAS-DB integrates genomic, proteomic, and genetic data from multiple studies in maize dealing with aflatoxin accumulation or Aspergillus flavus resistance., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 16 years ago - by Anonymous

In the Born Lab the goal is to seek to understand the circuitry of the mammalian cerebral cortex and how it endows us with the ability to see . . . and hear and think and talk. The approach is to study visual cortex of alert monkeys trained to report specific aspects of their visual experience. This allows us to define the neural correlates of specific percepts and then study their underlying mechanisms by activating or inactivating components of the circuit. Our primary tools are extracellular electrophysiologyboth with single electrodes and multi-electrode arraysand psychophysics. They are complemented by techniques that allow us to dissect and probe cortical circuitry: �� circuit tracing with genetically modified rabies viruses �� microstimulation to insert specific signals into cortical circuits �� cortical cooling (cryoloops) to reversibly inactivate circuit elements �� microarrays to identify molecular markers of neuronal subtypes �� optogenetics to improve the spatial and temporal specificity with which we can manipulate circuits Current Projects: *Dissecting parallel pathways. *Probing cortico-cortical feedback.

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• SciCrunch
• 16 years ago - by Anonymous

A platform for semantic data integration through RDF warehousing and efficient reasoning that helps to resolve conflicts in the data. Search and explore over 5 billion RDF statements from various sources including UniProt, PubMed, EntrezGene and 20 more... Perform complex SPARQL queries and retrieve more than one billion RDF resources. One of the major problems that biotechnology and pharmaceutical industries face today is how to combine data from multiple sources and make their research more productive. Data integration takes much time and often leads to errors and redundancies that require more time and resources to resolve. LinkedLifeData is a data warehouse that syndicates tons of heterogeneous biomedical knowledge in a common data model. The platform uses an extension of the RDF model that is able to track the provenance of each individual fact in the repository and thus update the information. Data Sources include: Disease Ontology, LinkedCT, Reactome, HPRD, DBPedia, UniProt, CellMap, NCBI Entrez-Gene, UMLS, IMID, MINT, DrugBank, LHGDN, Gene Ontology, HumanCYC, PubMed, NCI Nature, Human Phenotype Ontology, BioGRID, IntAct, HapMap, Symptom Ontology, DailyMed, ChEBI, Diseasome, Freebase, SIDER

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• SciCrunch
• 16 years ago - by Anonymous

Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health.

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• SciCrunch
• 16 years ago - by Anonymous

Microbiology news and views to help the busy scientist keep up-to-date on current research, forthcoming conferences, hot research topics, high impact publications, and much more.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE documented June 6, 2013 Database of all S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs. Curation of new and existing literature is ongoing and changes are incorporated weekly. User feedback is welcome. The genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824, has been sequenced and annotated. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.

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• SciCrunch
• 16 years ago - by Anonymous

The Museum of Comparative Anthropogeny (MOCA) is a collection of comparative information regarding humans and our closest evolutionary cousins (chimpanzees, bonobos, gorillas and orangutans i.e, great apes), with an emphasis on uniquely human features. MOCA is organized by Domains, each grouping Topics by areas of interest and scientific discipline. Each topic entry will eventually cover existing information about a particular difference (alleged or documented) between humans and non-human hominids. Comparisons of these non-human hominids with humans are difficult, as so little is known about their phenotypic features (phenomes), in contrast to humans. Ethical, fiscal and practical issues also limit collection of further information about great apes. MOCA attempts to collect existing information about human-specific differences from great apes, currently scattered in the literature. Having such information in one location could lead to new insights and multi-disciplinary interactions, and to ethically-sound studies to explain differences, and uniquely human specializations. MOCA is not targeted at experts in specific disciplines, but rather aims to communicate basic information to a broad audience of scientists from many backgrounds, and to the interested lay public. MOCA includes not only aspects wherein there are known or apparent differences between humans and great apes, but additionally, topics for which popular wisdom about claimed or assumed differences is not entirely correct. It is for all these reasons that MOCA is called a Museum, and not an Encyclopedia or Database.

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• SciCrunch
• 16 years ago - by Anonymous

A commercial organization which provides construction, architecture, engineering, and ecological services to private and public sector clients in Malaysia and overseas. The main focus of the Renexus Group is to incorporate sustainability in the projects they service. The Group provides services for both small and large scale projects, from project inception and development to commissioning and support services.

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• SciCrunch
• 16 years ago - by Anonymous

PrabiG is the Grenoble portal of the Prabi (Rhone-Alpes Bioinformatics Center) platform. It aims at providing the scientific community with tools and data related to proteomics and metabolomics. PrabiG is currently hosting the following projects : * UniPathway * ProteHome * OBIWarehouse * AT_Chloro

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• SciCrunch
• 16 years ago - by Anonymous