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239
UniProt: the Universal Protein Knowledgebase
- NUCLEIC ACIDS RES
, 2004
"... To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide ..."
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Cited by 335 (27 self)
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To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online
SCOP database in 2004: refinements integrate structure and sequence family data
, 2004
"... The Structural Classication of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classied into families, superfamilies, folds and classes. The continual acc ..."
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Cited by 273 (9 self)
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The Structural Classication of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classied into families, superfamilies, folds and classes. The continual accumulation of sequence and structural data allows more rigorous analysis and provides important information for understanding the protein world and its evolutionary repertoire. SCOP participates in a project that aims to rationalize and integrate the data on proteins held in several sequence and structure databases. As part of this project, starting with release 1.63, we have initiated a renement of the SCOP classication, which introduces a number of changes mostly at the levels below superfamily. The pending SCOP reclassication will be carried out gradually through a number of future releases. In addition to the expanded set of static links to external resources, available at the level of domain entries, we have started modernization of the interface capabilities of SCOP allowing more dynamic links with other databases. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.
The Gene Ontology Annotation (GOA) Database: Sharing knowledge in Uniprot with Gene Ontology
- Nucleic Acids Res 32: D262–D266. PLoS Biology | www.plosbiology.org March 2006 | Volume 4 | Issue 3 | e83
, 2004
"... The Gene Ontology Annotation (GOA) database ..."
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MIPS: analysis and annotation of proteins from whole genomes
- Nucleic Acids Res
, 2004
"... resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of.400 genomes automatically annotated w ..."
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Cited by 206 (14 self)
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resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of.400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein– protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server
BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark
- Proteins
, 2005
"... ABSTRACT Multiple sequence alignment is one of the cornerstones of modern molecular biology. It is used to identify conserved motifs, to determine protein domains, in 2D/3D structure prediction by homology and in evolutionary studies. Recently, high-throughput technologies such as genome sequencing ..."
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Cited by 129 (2 self)
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ABSTRACT Multiple sequence alignment is one of the cornerstones of modern molecular biology. It is used to identify conserved motifs, to determine protein domains, in 2D/3D structure prediction by homology and in evolutionary studies. Recently, high-throughput technologies such as genome sequencing and structural proteomics have lead to an explosion in the amount of sequence and structure information available. In response, several new multiple alignment methods have been developed that improve both the efficiency and the quality of protein alignments. Consequently, the benchmarks used to evaluate and compare these methods must also evolve. We present here the latest release of the most widely used multiple alignment benchmark, BAliBASE, which provides high quality, manually refined, reference alignments based on 3D structural superpositions. Version 3.0 of BAliBASE includes new, more challenging test cases, representing the real problems encountered when aligning large sets of complex sequences. Using a novel, semiautomatic update protocol, the number of protein families in the benchmark has been increased and representative test cases are now available that cover most of the protein fold space. The total number of proteins in BAliBASE has also been significantly increased from 1444 to 6255 sequences. In addition, full-length sequences are now provided for all test cases, which represent difficult cases for both global and local alignment programs. Finally, the BAliBASE Web site
MEROPS: the peptidase database
- Nucleic Acids Res
, 2004
"... Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotech-nology. The MEROPS database ..."
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Cited by 128 (4 self)
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Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotech-nology. The MEROPS database
Recent improvements to the PROSITE database
- Nucleic Acids Research
, 2004
"... The PROSITE database consists of a large collec-tion of biologically meaningful signatures that are described as patterns or pro®les. Each signature is linked to documentation that provides useful bio-logical information on the protein family, domain or functional site identi®ed by the signature. Th ..."
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Cited by 122 (9 self)
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The PROSITE database consists of a large collec-tion of biologically meaningful signatures that are described as patterns or pro®les. Each signature is linked to documentation that provides useful bio-logical information on the protein family, domain or functional site identi®ed by the signature. The PROSITE web page has been redesigned and several tools have been implemented to help the user discover new conserved regions in their own proteins and to visualize domain arrangements. We also introduced the facility to search PDB with a PROSITE entry or a user's pattern and visualize matched positions on 3D structures. The latest
SMART 4.0: towards genomic data integration
- Nucleic Acids Res
, 2004
"... SMART (Simple Modular Architecture Research Tool) is a web tool ..."
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Cited by 117 (7 self)
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SMART (Simple Modular Architecture Research Tool) is a web tool
GlobPlot: exploring protein sequences for globularity and disorder. Nucl Acids Res
, 2003
"... ABSTRACT A major challenge in the proteomics and structural genomics era is to predict protein structure and function, including identification of those proteins that are partially or wholly unstructured. Nonglobular sequence segments often contain short linear peptide motifs (e.g. SH3-binding site ..."
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Cited by 117 (2 self)
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ABSTRACT A major challenge in the proteomics and structural genomics era is to predict protein structure and function, including identification of those proteins that are partially or wholly unstructured. Nonglobular sequence segments often contain short linear peptide motifs (e.g. SH3-binding sites) which are important for protein function. We present here a new tool for discovery of such unstructured, or disordered regions within proteins. GlobPlot (http:// globplot.embl.de) is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder. We show examples with known proteins where it successfully identifies inter-domain segments containing linear motifs, and also apparently ordered regions that do not contain any recognised domain. GlobPlot may be useful in domain hunting efforts. The plots indicate that instances of known domains may often contain additional N-or C-terminal segments that appear ordered. Thus GlobPlot may be of use in the design of constructs corresponding to globular proteins, as needed for many biochemical studies, particularly structural biology. GlobPlot has a pipeline interface-GlobPipe-for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity.
