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Amos Marc Bairoch

Bio: Amos Marc Bairoch is a academic researcher from Swiss Institute of Bioinformatics. The author has contributed to research in topic(s): UniProt & PROSITE. The author has an hindex of 96, co-authored 222 publication(s) receiving 74599 citation(s). Previous affiliations of Amos Marc Bairoch include Ludwig Institute for Cancer Research & Carnegie Mellon University.

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Topics: UniProt, PROSITE, Proteome ...read more
Papers
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Book ChapterDOI: 10.1385/1-59259-584-7:531
Abstract: Protein identification and analysis software performs a central role in the investigation of proteins from two-dimensional (2-D) gels and mass spectrometry. For protein identification, the user matches certain empirically acquired information against a protein database to define a protein as already known or as novel. For protein analysis, information in protein databases can be used to predict certain properties about a protein, which can be useful for its empirical investigation. The two processes are thus complementary. Although there are numerous programs available for those applications, we have developed a set of original tools with a few main goals in mind. Specifically, these are: 1. To utilize the extensive annotation available in the Swiss-Prot database wherever possible, in particular the position-specific annotation in the Swiss-Prot feature tables to take into account posttranslational modifications and protein processing. 2. To develop tools specifically, but not exclusively, applicable to proteins prepared by two dimensional gel electrophoresis and peptide mass fingerprinting experiments. 3. To make all tools available on the World-Wide Web (WWW), and freely usable by the scientific community. In this chapter we give details about protein identification and analysis software that is available through the ExPASy World Wide Web server.

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Topics: Protein structure database (61%), ExPASy (54%)

6,688 Citations


Open accessJournal ArticleDOI: 10.1093/NAR/GKH131
Abstract: 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 (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.

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Topics: UniProt (68%)

6,522 Citations


Open accessJournal ArticleDOI: 10.1093/NAR/GKI070
Abstract: The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks.

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Topics: Universal Protein Resource (81%), UniProt (71%), Sequence database (64%)

3,934 Citations


Open accessJournal ArticleDOI: 10.1093/NAR/GKG563
Abstract: The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.

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Topics: ExPASy (66%), PROSITE (54%)

3,742 Citations


Open accessJournal ArticleDOI: 10.1093/NAR/GKG095
Abstract: The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org.

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Topics: UniProt (52%), Annotation (51%)

3,129 Citations


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Open accessJournal ArticleDOI: 10.1093/NAR/25.17.3389
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

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Topics: Substitution matrix (57%), Sequence database (54%), Sequence profiling tool (53%) ...read more

66,744 Citations


Open accessJournal ArticleDOI: 10.1093/NAR/22.22.4673
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

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Topics: Gap penalty (62%), Multiple sequence alignment (61%), Structural alignment (58%) ...read more

61,038 Citations


Open accessJournal ArticleDOI: 10.1038/75556
01 May 2000-Nature Genetics
Abstract: Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

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30,473 Citations


Open accessJournal ArticleDOI: 10.1093/NAR/28.1.235
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

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30,190 Citations


Open accessJournal ArticleDOI: 10.1002/JCC.20084
Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

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  • Figure 5. Density map for rice dwarf virus P8 capsid protein shown as a mesh (left). The map was obtained by electron cryo-microscopy and has 6.8-Å resolution.49 Computationally identified alpha helices are shown as cylinders50 and the connecting turns have been hand traced using Chimera’s Volume Path Tracer. On the right is a crystal structure of the distantly related bluetongue virus capsid protein (1bvp51).
    Figure 5. Density map for rice dwarf virus P8 capsid protein shown as a mesh (left). The map was obtained by electron cryo-microscopy and has 6.8-Å resolution.49 Computationally identified alpha helices are shown as cylinders50 and the connecting turns have been hand traced using Chimera’s Volume Path Tracer. On the right is a crystal structure of the distantly related bluetongue virus capsid protein (1bvp51).
  • Figure 6. Fluorescently labeled Drosophila chromosome imaged by wide-field deconvolution microscopy (M. Lowenstein and J. Sedat, UCSF, unpublished data). Three fluorophores were used to label specific segments of chromosome 2L. Two homologous copies of the chromosome are shown. The cyan isosurface is the nuclear envelope. The individual fluorescent spots have been marked with the Volume Path Tracer extension and paths connecting the markers are shown as smooth tubes. Traced structures from many cells can be clustered to study structural patterns of chromosome organization in the nucleus.
    Figure 6. Fluorescently labeled Drosophila chromosome imaged by wide-field deconvolution microscopy (M. Lowenstein and J. Sedat, UCSF, unpublished data). Three fluorophores were used to label specific segments of chromosome 2L. Two homologous copies of the chromosome are shown. The cyan isosurface is the nuclear envelope. The individual fluorescent spots have been marked with the Volume Path Tracer extension and paths connecting the markers are shown as smooth tubes. Traced structures from many cells can be clustered to study structural patterns of chromosome organization in the nucleus.
  • Figure 4. The ViewDock interface lists docked molecules; clicking on a line displays just the corresponding molecule and shows its information in the lower part of the panel. Ribose monophosphate is shown docked to H-Ras (121p48). Carbon atoms are light gray, oxygen atoms are red, nitrogen atoms are blue, and phosphorus atoms are cyan. Hydrogens are not shown. Potential hydrogen bonds are indicated with yellow lines.
    Figure 4. The ViewDock interface lists docked molecules; clicking on a line displays just the corresponding molecule and shows its information in the lower part of the panel. Ribose monophosphate is shown docked to H-Ras (121p48). Carbon atoms are light gray, oxygen atoms are red, nitrogen atoms are blue, and phosphorus atoms are cyan. Hydrogens are not shown. Potential hydrogen bonds are indicated with yellow lines.
  • Figure 3. Three structures in Chimera associated with sequences in an alignment shown by Multalign Viewer. The sequences with color swatches behind their names are associated with the pectate lyase structures 1jta,45 1bn8,46 and 2pec47 (shown in yellow, magenta, and cyan, respectively). The structures were superimposed using the sequence alignment; the fits were refined by iteratively removing bad residue pairings. The sequences are colored by secondary structure (strand and helix regions are pink and gold, respectively) and selected structure regions are green (indicated on the structures with a green outline). Chimera’s zone selection method was used to select all residues within 3.6 Å of the active-site metal ion in one of the structures.
    Figure 3. Three structures in Chimera associated with sequences in an alignment shown by Multalign Viewer. The sequences with color swatches behind their names are associated with the pectate lyase structures 1jta,45 1bn8,46 and 2pec47 (shown in yellow, magenta, and cyan, respectively). The structures were superimposed using the sequence alignment; the fits were refined by iteratively removing bad residue pairings. The sequences are colored by secondary structure (strand and helix regions are pink and gold, respectively) and selected structure regions are green (indicated on the structures with a green outline). Chimera’s zone selection method was used to select all residues within 3.6 Å of the active-site metal ion in one of the structures.
Topics: Unix (50%), OS X (50%)

28,452 Citations


Performance
Metrics

Author's H-index: 96

No. of papers from the Author in previous years
YearPapers
20211
20205
20192
20187
20173
20163

Top Attributes

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Author's top 5 most impactful journals

Nucleic Acids Research

54 papers, 43.8K citations

Electrophoresis

13 papers, 1.5K citations

Bioinformatics

8 papers, 716 citations

Database

8 papers, 168 citations

Proteomics

7 papers, 406 citations

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