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Results for “reference protein database”

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PubMed2004

CDtool-an integrated software package for circular dichroism spectroscopic data processing, analysis, and archiving.

CDtool is a software package written to facilitate circular dichroism (CD) spectroscopic studies on both conventional lab-based instruments and synchrotron beamlines. It takes format-independent input data from any type of CD instrument, enables a wide range of standard and advanced processing methods, and, in a single user-friendly graphics-based package, takes raw data through the entire processing procedure and, importantly, uses data-mining techniques to retain in the final output all the information associated with the processing. It permits the facile comparison of data obtained from different instruments without the need for reformatting and displays it in graphical formats suitable for publication. It also includes the ability to automatically archive the processed data. This latter feature may be especially useful in light of recent funding institution directives with regard to data sharing and archiving and requirements for "good practice" and "traceability" within the pharmaceutical industry. In addition, CDtool includes a means of interfacing with protein data bank coordinate files and calculating secondary structures from them using alternate definitions and algorithms. This feature, along with a function that permits the facile production of new reference databases, enables the creation of specialized databases for secondary structural analyses of specific types of proteins. Thus the CDtool software not only enables rapid data processing and analyses but also includes many enhanced features not available in other CD data processing/analysis packages.

Archives↗

PubMed2006

Phytome: a platform for plant comparative genomics.

Phytome is an online comparative genomics resource that can be applied to functional plant genomics, molecular breeding and evolutionary studies. It contains predicted protein sequences, protein family assignments, multiple sequence alignments, phylogenies and functional annotations for proteins from a large, phylogenetically diverse set of plant taxa. Phytome serves as a glue between disparate plant gene databases both by identifying the evolutionary relationships among orthologous and paralogous protein sequences from different species and by enabling cross-references between different versions of the same gene curated independently by different database groups. The web interface enables sophisticated queries on lineage-specific patterns of gene/protein family proliferation and loss. This rich dataset is serving as a platform for the unification of sequence-anchored comparative maps across taxonomic families of plants. The Phytome web interface can be accessed at the following URL: http://www.phytome.org. Batch homology searches and bulk downloads are available upon free registration.

Databases, Genetic↗

PubMed2000

An automatic homology modeling method consisting of database searches and simulated annealing.

We introduce a method of homology modeling consisting of database searches and simulated annealing. All processes involving searches for homologous proteins, alignment, the construction of Calpha atoms, construction of main-chain atoms, and the construction of side-chain atoms are performed automatically. In this method, main-chain conformations are generated from the weighted average of mainchain coordinates in reference proteins. The weight is defined by the local space homology representing the similarity of environmental residues at topologically equivalent positions in reference proteins. Side-chain conformations are generated for constructed main-chain atoms by database searches, and main-chain atoms are optimized for the fixed side-chain conformations. These two processes, i.e., the side-chain generation and main-chain optimization, are repeated several times. This type of construction provides a structure similar to the x-ray structure, in particular, for main-chain and side-chain atoms in the residues belonging to structurally conserved regions (SCRs). The accuracy of our method was evaluated for 14 proteins whose structures are known. The average root mean square deviation between models and x-ray structures was 2.29 A for all atoms, and the percentage of chi1 angles within 30 degrees was 72.6% for SCRs residues. Some models were in good agreement with their respective x-ray structures. Our method, which has the advantage of being automated, gives results similar to, or better than, published results for three widely used test proteins. Our software, FAMS, is available on the World Wide Web.

Amino Acid Sequence↗

PubMed2006

Gene and protein nomenclature in public databases.

BACKGROUND: Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap. RESULTS: We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human) from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism. CONCLUSION: In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of combined dictionaries considerably increases size and decreases ambiguity. The entries of the curated synonym dictionary are available for manual querying, editing, and PubMed- or Google-search via the ProThesaurus-wiki. For automated querying via custom software, we offer a web service and an exemplary client application.

Abstracting and Indexing↗

PubMed2006

Protein kinase resource: an integrated environment for phosphorylation research.

The protein kinase superfamily is an important group of enzymes controlling cellular signaling cascades. The increasing amount of available experimental data provides a foundation for deeper understanding of details of signaling systems and the underlying cellular processes. Here, we describe the Protein Kinase Resource, an integrated online service that provides access to information relevant to cell signaling and enables kinase researchers to visualize and analyze the data directly in an online environment. The data set is synchronized with Uniprot and Protein Data Bank (PDB) databases and is regularly updated and verified. Additional annotation includes interactive display of domain composition, cross-references between orthologs and functional mapping to OMIM records. The Protein Kinase Resource provides an integrated view of the protein kinase superfamily by linking data with their visual representation. Thus, human kinases can be mapped onto the human kinome tree via an interactive display. Sequence and structure data can be easily displayed using applications developed for the PKR and integrated with the website and the underlying database. Advanced search mechanisms, such as multiparameter lookup, sequence pattern, and blast search, enable fast access to the desired information, while statistics tools provide the ability to analyze the relationships among the kinases under study. The integration of data presentation and visualization implemented in the Protein Kinase Resource can be adapted by other online providers of scientific data and should become an effective way to access available experimental information.

Amino Acid Sequence↗

PubMed2005

A two-dimensional electrophoresis reference map of human ovary.

The ovary plays a central role in oogenesis and gonadal hormone secretion. Proteomic analysis is a valuable approach for gaining an increased understanding of the molecular nature of the ovary. In this work, two-dimensional electrophoresis for protein separation followed by matrix-assisted laser desorption/ionization mass spectrometry and database searches, identified 231 protein spots corresponding to 138 individual proteins that were found in gels representing both the follicular and luteal phases. The data were used to construct a database online (http://reprod.njmu.edu.cn/2d). The identified proteins were functionally classified into seven groups: (1) cell signaling/communication, (2) cell division, (3) gene/protein expression, (4) metabolism, (5) cell structure and motility, (6) cell/organism defense, and (7) unclassified. Among the proteins identified, 47% had not been previously reported in the human ovary. In addition, a number of disease-related proteins were identified in this protein map, including some cancer- and polycystic ovarian syndrome-related proteins. Two proteins with phosphorylation were verified by Western blot analysis. Comparison of protein abundance between follicular and luteal stages produced seven protein spots that had been identified in our database. This study provides a preliminary reference map of normal human ovary that will form a basis for comparative studies on normal and pathological conditions of the human ovary and may serve as a potential tool for clinical diagnosis, therapeutics, and prognosis.

Animals↗

PubMed2004

The Human Proteome Organization Plasma Proteome Project pilot phase: reference specimens, technology platform comparisons, and standardized data submissions and analyses.

A comprehensive, systematic characterization of cirolating proteins in health and disease will greatly facilitate development of biomarkers for prevention, diagnosis, and therapy of cancers and other diseases. The Human Proteome Organization Plasma Proteome Project pilot phase aims to (1) compare the advantages and limitations of many technology platforms; (2) contrast reference specimens of human plasma (ethylenediaminetetra acetic acid, heparin, citrate-anticoagulated) and serum, in terms of numbers of proteins identified and any interferences with various technology platforms; and (3) create a global knowledge base/data repository.

Biomarkers↗

PubMed2001

A reference map of human lung MRC-5 fibroblast proteins using immobilized pH gradient-isoelectric focusing-based two-dimensional electrophoresis.

We report the first protein map of human adult lung MRC-5 fibroblasts using isoelectric focusing-immobilized pH gradient-based two-dimensional polyacrylamide gel electrophoresis. MRC-5 is an immortalised cell line used in a wide range of investigations. The two-dimensional gel pattern of proteins generated from any given cell system provides a fingerprint that is unique to those cells. Therefore, the establishment of a protein map for a particular cell system provides a useful reference tool as a "master map" for subsequent studies using those cells. In this map a total of 98 protein spots were identified by comparative searches of the nucleotide and protein database using peptide masses obtained by matrix-assisted laser desorption/ionization time of flight following trypsin digestion. To increase the utility of the reference map, cells were cultured in both Dulbecco's modified Eagle medium (DMEM), the standard medium, and Roswell Park Memorial Institute (RPMI)-1640. Two-dimensional gel protein patterns of MRC-5 cultures were shown to be largely unaffected by the use of RPMI compared to DMEM, respectively. In combination with the reference map, the standardised protocol described provides a tool for comparative studies involving MRC-5 cells in which nonspecific variation is minimized.

Adult↗

PubMed2003

SDAP: database and computational tools for allergenic proteins.

SDAP (Structural Database of Allergenic Proteins) is a web server that provides rapid, cross-referenced access to the sequences, structures and IgE epitopes of allergenic proteins. The SDAP core is a series of CGI scripts that process the user queries, interrogate the database, perform various computations related to protein allergenic determinants and prepare the output HTML pages. The database component of SDAP contains information about the allergen name, source, sequence, structure, IgE epitopes and literature references and easy links to the major protein (PDB, SWISS-PROT/TrEMBL, PIR-ALN, NCBI Taxonomy Browser) and literature (PubMed, MEDLINE) on-line servers. The computational component in SDAP uses an original algorithm based on conserved properties of amino acid side chains to identify regions of known allergens similar to user-supplied peptides or selected from the SDAP database of IgE epitopes. This and other bioinformatics tools can be used to rapidly determine potential cross-reactivities between allergens and to screen novel proteins for the presence of IgE epitopes they may share with known allergens. SDAP is available via the World Wide Web at http://fermi.utmb.edu/SDAP/.

Allergens↗

PubMed1995

An updated two-dimensional gel database of rat liver proteins useful in gene regulation and drug effect studies.

We have improved upon the reference two-dimensional (2-D) electrophoretic map of rat liver proteins originally published in 1991 (N. L. Anderson et al., Electrophoresis 1991, 12, 907-930). A total of 53 proteins (102 spots) are now identified, many by microsequencing. In most cases, spots cut from wet, Coomassie Blue stained 2-D gels were submitted to internal tryptic digestion [2], and individual peptides, separated by high-performance liquid chromatography (HPLC), were sequenced using a Perkin-Elmer 477A sequenator. Additional spots were identified using specific antibodies.

Animals↗

PubMed2001

Cytochrome P450 database.

This paper describes a specialized database dedicated exclusively to the cytochrome P450 superfamily. The system provides the impression of superfamily's nomenclature and describes structure and function of different P450 enzymes. Information on P450-catalyzed reactions, substrate preferences, peculiarities of induction and inhibition is available through the database management system. Also the source genes and appropriate translated proteins can be retrieved together with corresponding literature references. Developed programming solution provides the flexible interface for browsing, searching, grouping and reporting the information. Local version of database manager and required data files are distributed on a compact disk. Besides, there is a network version of the software available on Internet. The network version implies the original mechanism, which is useful for the permanent online extension of the data scope.

Catalysis↗

PubMed1999

The SWISS-2DPAGE database: what has changed during the last year.

SWISS-2DPAGE (http://www.expasy.ch/ch2d/) is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database established in 1993. The current release contains 21 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps now have 2480 identified spots, corresponding to 528 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence. During the last year, the SWISS-2DPAGE has undergone major changes. Six new maps have been added, and new functions to access the data have been provided through the ExPASy server. Finally, an important change concerns the database funding source.

Animals↗

PubMed1998

MHCPEP, a database of MHC-binding peptides: update 1997.

MHCPEP (http://wehih.wehi.edu.au/mhcpep/) is a curated database comprising over 13 000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains the peptide sequence, its MHC specificity and where available, experimental method, observed activity, binding affinity, source protein and anchor positions, as well as publication references. The present format of the database allows text string matching searches but can easily be converted for use in conjunction with sequence analysis packages. The database can be accessed via Internet using WWW or FTP.

Amino Acid Sequence↗

PubMed2005

Dasty and UniProt DAS: a perfect pair for protein feature visualization.

In this study, we present two freely available and complementary Distributed Annotation System (DAS) resources: a DAS reference server that provides up-to-date sequence and annotation from UniProt, with additional feature links and database cross-references from InterPro and a DAS client implemented using Java and Macromedia Flash that is optimized for the display of protein features.

Algorithms↗

PubMed2001

Establishment of a root proteome reference map for the model legume Medicago truncatula using the expressed sequence tag database for peptide mass fingerprinting.

We have established a proteome reference map for Medicago truncatula root proteins using two-dimensional gel electrophoresis combined with peptide mass fingerprinting to aid the dissection of nodulation and root developmental pathways by proteome analysis. M. truncatula has been chosen as a model legume for the study of nodulation-related genes and proteins. Over 2,500 root proteins could be displayed reproducibly across an isoelectric focussing range of 4-7. We analysed 485 proteins by peptide mass fingerprinting, and 179 of those were identified by matching against the current M. truncatula expressed sequence tag (EST) database containing DNA sequences of approximately 105,000 ESTs. Matching the EST sequences to available plant DNA sequences by BLAST searches enabled us to predict protein function. The use of the EST database for peptide identification is discussed. The majority of identified proteins were metabolic enzymes and stress response proteins, and 44% of proteins occurred as isoforms, a result that could not have been predicted from sequencing data alone. We identified two nodulins in uninoculated root tissue, supporting evidence for a role of nodulins in normal plant development. This proteome map will be updated continuously (http://semele.anu.edu.au/2d/2d.html) and will be a powerful tool for investigating the molecular mechanisms of root symbioses in legumes.

Databases as Topic↗

PubMed2004

Kidney gene database: a curated and integrated database of genes involved in kidney disease.

PURPOSE: We have created a curated and integrated database, the Kidney Gene Database (KGDB) (http://www.urogene.org/kgdb) that contains current information about genes or genomic loci involved in human kidney disease. MATERIALS AND METHODS: Genes that undergo molecular, genetic or epigenetic events that affect kidney function are identified through a biomedical literature search and catalogued in the database. RESULTS: Events that are currently screened for are gene amplification, mutation, deletion, polymorphism, loss of heterozygosity, DNA methylation and DNA hypomethylation. In addition, genes that are uniquely expressed in the kidney, as determined by analyzing the expressed sequence tags database and the Serial Analysis of Gene Expression database, are also included in KGDB. For each gene KGDB provides basic information about the gene product, a tissue type gene expression profile, links to protein, mRNA and genomic DNA sequence information, relevant literature citations and cross-references to other databases. CONCLUSIONS: We present KGDB, which is to our knowledge the first curated and integrated database of genes involved in human kidney disease. KGDB is free, widely accessible and easy to use, and it provides a wealth of relevant information. In addition, KGDB will be continuously updated every 6 months to include new information published in the biomedical literature or in gene expression databases. We envision that KGDB will serve as a valuable resource for scientists and clinicians.

Databases, Genetic↗

PubMed2004

TAFA: a novel secreted family with conserved cysteine residues and restricted expression in the brain.

We have discovered a family of small secreted proteins in Homo sapiens and Mus musculus using a novel database searching strategy. The family is composed of five highly homologous genes referred to as TAFA-1 to -5. The TAFA genes encode proteins of approximately 100 amino acids that contain conserved cysteine residues at fixed positions. TAFA-1 to -4 are more closely related to each other than to TAFA-5, in which a conserved motif including CC in TAFA-1 to -4 is not present. In H. sapiens, TAFA-3 has two isoforms formed by alternative splicing. Sequence homology analyses reveal that TAFA proteins appear distantly related to MIP-1alpha, a member of the CC-chemokine family. TAFA mRNAs are highly expressed in specific brain regions, with little expression seen in other tissues.

Alternative Splicing↗

PubMed1998

Two-dimensional electrophoresis for analysis of Mycobacterium tuberculosis culture filtrate and purification and characterization of six novel proteins.

Culture filtrate from Mycobacterium tuberculosis contains molecules which promote high levels of protective immunity in animal models of subunit vaccination against tuberculosis. We have used two-dimensional electrophoresis for analysis and purification of six novel M. tuberculosis culture filtrate proteins (CFPs): CFP17, CFP20, CFP21, CFP22, CFP25, and CFP28. The proteins were tested for recognition by M. tuberculosis-reactive memory cells from different strains of inbred mice and for their capacity to induce a skin test response in M. tuberculosis-infected guinea pigs. CFP17, CFP20, CFP21 and CFP25 induced both a high gamma interferon release and a strong delayed-type hypersensitivity response, and CFP21 was broadly recognized by different strains of inbred mice. N-terminal sequences were obtained for the six proteins, and the corresponding genes were identified in the Sanger M. tuberculosis genome database. In parallel we established a two-dimensional electrophoresis reference map of short-term culture filtrate components and mapped novel proteins as well as already-known CFP.

Amino Acid Sequence↗