Nucleic Acids Research, 2003, Vol. 31, No. 13 3784-3788
© 2003 Oxford University Press
ExPASy: the proteomics server for in-depth protein knowledge and analysis
Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
*To whom correspondence should be addressed. Tel: +41 22 379 5050; Fax: +41 22 379 5858; Email: elisabeth.gasteiger{at}isb-sib.ch
Received February 18, 2003; Revised and Accepted April 2, 2003
| ABSTRACT |
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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.
| INTRODUCTION |
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The Swiss Institute of Bioinformatics (SIB, http://www.isb-sib.ch) is an academic not-for-profit foundation whose mission is to promote research, the development of databanks and computer technologies, teaching and service activities in the field of bioinformatics. One of the SIB's windows to the world is the ExPASy server, which focuses on proteins and proteomics, and provides access to a variety of databases and analysis tools. One of the major assets of ExPASy is the high degree of integration and interconnectivity that it establishes between all the available databases and services. Rather than just making each service accessible in an isolated manner, we put at the disposal of the users different expert views of the complex world of biological data and knowledge.
| DATABASES |
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ExPASy (1,2) is the main host for the following databases that are partially or completely developed at the SIB in Geneva:
- The SWISS-PROT knowledgebase (3,4) (http://www.expasy.org/sprot/) is a curated protein sequence database, which strives to provide high quality annotations (such as the description of the function of a protein, its domain structure, post-translational modifications and variants), a minimal level of redundancy and a high level of integration with other databases. SWISS-PROT is supplemented by TrEMBL, which contains computer-annotated entries for all sequences not yet integrated in SWISS-PROT. SWISS-PROT and TrEMBL are maintained collaboratively by the SIB and the European Bioinformatics Institute (EBI).
- SWISS-2DPAGE (5) (http://www.expasy.org/ch2d/) is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2D PAGE). SWISS-2DPAGE contains data from a variety of human and mouse biological samples as well as from Arabidopsis thaliana, Escherichia coli, Saccharomyces cerevisiae and Dictyostelium discoideum.
- PROSITE (6,7) (http://www.expasy.org/prosite/) is a database of protein domains and families. PROSITE contains biologically significant sites, patterns and profiles that help to reliably identify to which known protein family a new sequence belongs.
- ENZYME (8) (http://www.expasy.org/enzyme/) is a repository of information relative to the nomenclature of enzymes.
- SWISS-MODEL Repository (9) (http://www.expasy.org/swissmod/smrep.html) is a database of automatically generated structural protein models.
Cross-references
All the databases available on ExPASy are extensively cross-referenced to other molecular biology databases or resources all over the world. SWISS-PROT for example is explicitly cross-referenced (10) to
50 different databases specializing in protein and nucleic acid sequences, 3D-structure, organism-specific and genomic information, domain and family signatures, post-translational modifications or proteomics data. Examples for databases currently linked to SWISS-PROT in that manner are EMBL/GenBank/DDBJ, PDB, FlyBase, MGD, MIM, MypuList, SGD, SubtiList, TubercuList, WormPep, ZFIN, InterPro, Pfam, PRINTS, ProDom, PROSITE, SMART, TIGRFAMs, SWISS-2DPAGE, HSSP, MEROPS and REBASE. On average, a SWISS-PROT entry contains 7.8 explicit cross-references to other databases (release 40.43 of 12 February 2003). Literature references for the above-mentioned databases are listed in the SWISS-PROT user manual, (http://www.expasy.org/sprot/userman.html#DR_line).
Complementing these explicit cross-references, so-called implicit links to
25 additional resources are created on-the-fly by the NiceProt view of SWISS-PROT and TrEMBL entries (see below). This concept is targeted at data collections that do not have their own system of unique identifiers, but can be referenced via identifiers such as SWISS-PROT or EMBL accession numbers, gene names, etc. Examples for databases linked to SWISS-PROT via implicit links are those that are based on SWISS-PROT and provide a specific analytical view of each entry (e.g. ProDomautomatically derived domain views or ProtoMapa hierarchical classification of all SWISS-PROT entries) and those databases that share some identifier with SWISS-PROT (e.g. GeneCardsinformation on human genes, accessible by the HUGO approved gene name). Implicit links are a specific feature of ExPASy and are not available on other web servers, or in the SWISS-PROT/TrEMBL data files that can be downloaded by ftp. They greatly enhance database interoperability and strengthen the role of SWISS-PROT as a central hub for the interconnection of biomolecular resources.
Update frequency and download options
SWISS-PROT, PROSITE, ENZYME and SWISS-2DPAGE are updated at a frequency of
12 weeks.
For all the ExPASy databases, data and associated documentation files can be copied locally by anonymous FTP (ftp.expasy.org). In particular, the different download options for the SWISS-PROT and TrEMBL databases, including the different available subsections, release frequencies and data formats, are documented at http://www.expasy.org/sprot/download.html. Among others, we distribute the files to assemble a non-redundant and complete protein sequence database (ftp://ftp.expasy.org/databases/sp_tr_nrdb/) consisting of three components: SWISS-PROT, TrEMBL and new entries to be later integrated into TrEMBL (known as TrEMBLnew). These files are supplemented by a compilation of sequences for splice variants, reconstructed from the annotations in SWISS-PROT and TrEMBL feature tables. All these files are completely rebuilt every time SWISS-PROT is updated.
A large variety of documents (user manual, release notes, indices, nomenclature documents, etc.) are available with SWISS-PROT; these documents can all be browsed from ExPASy (http://www.expasy.org/sprot/sp-docu.html) and are enhanced by a variety of hyperlinks.
No fees for academic users
The use of all ExPASy databases is free for academic users. However, we implemented in September 1998 a system of annual subscription fee for commercial users of the SWISS-PROT, PROSITE and SWISS-2DPAGE databases. The funds raised are used to bring these databases up-to-date, to keep them up-to-date and to further enhance their quality. Further information on this funding scheme is available at http://www.expasy.org/announce/.
| SOFTWARE TOOLS |
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We have developed, over the years, an extensive collection of software tools, most of which are either targeted toward the access and display of the databases mentioned above, or can be used to analyze protein sequences and proteomics data originating from 2D-PAGE and mass spectrometry experiments. These latter tools can all be accessed from ExPASy (http://www.expasy.org/tools/).
Database query, display and navigation
A variety of query options are available from the home pages of each of the ExPASy databases. These options allow the users to display and retrieve specified subsets of the database. For example, from the home page of SWISS-PROT and TrEMBL, different query forms allow searching by description, accession number, author, citation or by full text search. To complement these options, we have also implemented an SRS (11) server that allows complex searches on any fields of the combination of SWISS-PROT and TrEMBL databases. PROSITE, ENZYME and SWISS-2DPAGE can also be queried using SRS.
The original flat file format of all ExPASy databases is based on different line types, where a two-letter line code defines the information contained on the rest of that line (e.g. for SWISS-PROT: see the user manual, http://www.expasy.org/sprot/userman.html). This format is easy to parse by computer programs, but not necessarily easy to read for human users. In order to provide a more verbose and user-friendly view of the database entries, we provide for each database, on ExPASy, a nice hypertext view, e.g. NiceProt for SWISS-PROT and TrEMBL entries. An example for an entry in the NiceProt view can be seen at http://www.expasy.org/cgi-bin/niceprot.pl?P57727, or in Figure 1. The figure shows parts of that entry in order to illustrate the easy navigation between information contained in the entry itself, the corresponding documentation, remote databases, and the submission forms or results of sequence alignment or other ExPASy analysis tools. Similar views are available for PROSITE (NiceSite and NiceDoc), ENZYME (NiceZyme) and SWISS-2DPAGE (Nice2Dpage).
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Swiss-Shop (http://www.expasy.org/swiss-shop/) is an automated sequence alerting system which allows users to obtain new SWISS-PROT entries relevant to their field(s) of interest. Keyword-based and sequence/pattern-based requests are possible. Every time a weekly SWISS-PROT release is performed, all new database entries matching the user-specified search keywords or patterns or the entries showing sequence similarities to the user-specified sequence are automatically sent to the user by email.
Sequence analysis tools
- BLAST (12) provides very fast similarity searches of a protein sequence against a protein or nucleotide database. The ExPASy BLAST service is maintained in collaboration with the Swiss EMBnet node on dedicated hardware. The native output of BLAST is extended with several original features (Fig. 1).
- ScanProsite (13) scans a sequence against all the patterns, profiles and rules in PROSITE or scans a pattern, profile or rule against all sequences in SWISS-PROT, TrEMBL and/or PDB.
- SWISS-MODEL (14,15) is an automated knowledge-based protein modelling server. It is able to build models for the 3D structure of proteins whose sequence is closely related to that of proteins with known 3D structure.
- ProtParam calculates physico-chemical parameters of a protein sequence such as the amino acid composition, the pl, the atomic composition, the extinction coefficient, etc.
- ProtScale computes and represents the profile produced by any amino acid scale on a selected protein. Some 50 predefined scales are available, such as the Doolittle and Kyte hydrophobicity scale.
- RandSeq generates a random protein sequence, based on a user-specified amino acid composition and sequence length.
- Sulfinator (16) predicts tyrosine sulfation sites within protein sequences.
- Translate translates a nucleotide sequence into a protein in six reading frames.
Proteomics tools
- AACompIdent (17) identifies a protein by its amino acid composition.
- AACompSim (17) finds for a given SWISS-PROT entry, the database entries which have the most similar amino acid composition.
- Compute pI/MW (18) computes the theoretical isoelectric point (pI) and molecular weight (MW) from a SWISS-PROT or TrEMBL entry or for a user sequence.
- FindMod (19) predicts potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified SWISS-PROT entry or from a user-entered sequence. Mass differences are used to better characterize the protein of interest.
- FindPept (20) identifies peptides resulting from unspecific cleavage of proteins by their experimental masses, taking into account artefactual chemical modifications, post-translational modifications and protease autolytic cleavage.
- GlycanMass calculates the mass of an oligosaccharide structure.
- GlycoMod (21) predicts possible oligosaccharide structures that occur on proteins from their experimentally determined masses. This is done by comparing the mass of a potential glycan to a list of pre-computed masses of glycan compositions.
- PeptideCutter predicts potential protease cleavage sites and sites cleaved by chemicals in a given protein sequence.
- PeptideMass (22) calculates the theoretical masses of peptides generated by the chemical or enzymatic cleavage of proteins so as to assist in the interpretation of peptide mass fingerprinting.
- PeptIdent, TagIdent, MultiIdent (2325), these three related programs identify proteins using a variety of experimental information such as the pI, the MW, the amino acid composition, partial sequence tags and peptide mass fingerprinting data.
A very important feature of the ExPASy proteomics tools (such as PeptIdent, TagIdent, MultiIdent, PeptideMass, FindPept or FindMod) is that, when performing their computations and predictions, they use the annotations relevant to post-translational modifications and processing, as well as splice variants documented in the SWISS-PROT feature tables.
These tools are all listed on a page on ExPASy (http://www.expasy.org/tools/) that also offers links to many other useful programs for the analysis of protein sequences available elsewhere on the web. We notably have links to the tools provided by our colleagues from the bioinformatics group at ISREC (http://www.isrec.isb-sib.ch) and the Swiss EMBnet node (http://www.ch.embnet.org) in Lausanne. They have developed a BLAST similarity search server, TMpred (to predict transmembrane regions) and interfaces to the SAPS (Statistical Analysis of Protein Sequences), COILS (prediction of coiled coil regions), Clustal and T-Coffee (multiple sequence alignment) programs.
| ExPASy AS A PORTAL TO OTHER LIFE SCIENCE RESOURCES |
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The mass of information available to life scientists on the web has completely changed the way in which biological data is accessed and processed. It has created many opportunities, but also brought new dangers. One of the most critical problems is the difficulty for researchers to distinguish useful and up-to-date sources of information from sites that provide either fossilized or low-quality data. To partially address this problem, we have developed a series of lists and tools:
- Amos' WWW links page (http://www.expasy.org/alinks.html) is a list that contains links to >1000 information resources for the life sciences. This list is updated very frequently and is organized in a number of sections that correspond to specific topics.
- WORLD-2DPAGE (http://www.expasy.org/ch2d/2d-index.html) is a list of all known 2D PAGE database WWW servers and related services.
- BioHunt (http://www.expasy.org/BioHunt/) is a service to help search the internet for molecular biology information. BioHunt is built by Marvin, a software robot which automatically roams the web to search and index life science and bioinformatics information. Currently BioHunt indexes
35 000 documents.
- 2DHunt (http://www.expasy.org/ch2d/2DHunt/) is a specialized index for 2D PAGE-related sites.
- ExPASy tools page (http://www.expasy.org/tools/), in addition to hosting the above-mentioned tools provided and maintained by the Swiss Institute of Bioinformatics, the tools page serves as a portal to useful web-accessible tools on bioinformatics servers elsewhere. Tools local to the ExPASy server are marked by the ExPASy logo.
- List of conferences and events (http://www.expasy.org/conf.html) is a list of conferences and meetings relevant to proteomics, bioinformatics and other domains in the life sciences.
| OTHER INTERESTING ExPASy FEATURES |
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- Biochemical pathways (http://www.expasy.org/tools/pathways/) is an indexed, digitized and clickable version of the Boehringer Mannheim's Biochemical Pathways poster and is available on the server. It allows the user to navigate through the graphical representation of metabolic pathways and is linked to the ENZYME database.
- DeepView (SWISS-PdbViewer) (15) (http://www.expasy.org/spdbv/) is an application running on the Microsoft Windows, Mac, SGI and Linux platforms, offering a wide range of options to visualize and manipulate protein structures. It can also be used as a WWW helper application for the display of PDB formatted entries. Swiss-PdbViewer can be downloaded from ExPASy and complements the aforementioned SWISS-MODEL homology-modeling tool.
- LALNVIEW (26) (http://www.expasy.org/tools/lalnview.html) is an application that runs on the Microsoft Windows, Mac and Unix platforms. LALNVIEW is a graphical viewer for pairwise sequence alignments. It can be used to display the results of a pairwise alignment carried out with the SIM (27) software also installed on ExPASy (http://www.expasy.org/tools/sim-prot.html).
- 2D PAGE: a wide variety of information concerning 2D PAGE is available from ExPASy. This includes the full description of experimental protocols as well as an overview of the Melanie 3 2D PAGE analysis software package. A 2D gel viewer is also available for download.
- Protein Spotlight (http://www.expasy.org/spotlight/) is a periodical review centered on a specific protein or group of proteins.
- Recreational. One must not forget that science can also have a lighter side. So we hope that users will take the time to take a small pause from the hectic pace of modern research and visit Swiss-Quiz (http://www.expasy.org/swiss-quiz/). With Swiss-Quiz one can have a chance to win some Swiss chocolate (real, not virtual!) after having successfully answered a quiz from the field of molecular biology.
- ExPASyBar is a useful navigation bar to the most important databases and tools on ExPASy. ExPASyBar was developed by Martin Hassman from the Institute of Chemical Technology in Prague, in collaboration with the ExPASy team. It is an add-on to the free Mozilla web browser (http://www.mozilla.org), and can be downloaded from http://expasybar.mozdev.org.
| MIRROR SITES |
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Network congestion and resulting slow response times represent a major problem for users in certain parts of the world. To help address this issue, we decided to implement mirror sites of ExPASy in various countries. Such sites can help users to access the ExPASy databases and tools more rapidly in locations that do not have a fast connection to Switzerland. The mirror sites are computers that host exact copies of the information available from the Geneva ExPASy server. They are updated at the same frequency as the main ExPASy site in Switzerland. ExPASy mirror sites are located in academic institutions that have shown an active interest in hosting such sites. As of today, seven sites are operational. The ExPASy mirror sites are located in:
- Australia: http://au.expasy.org/ at the Australian Proteome Analysis Facility (APAF), Sydney.
- Bolivia: http://bo.expasy.org/ at the Universidad Católica Boliviana (UCB), Cochabamba.
- Canada: http://ca.expasy.org/ at the Canadian Bioinformatics Resource (CBR), Halifax.
- China: http://cn.expasy.org/ at the Center of Bioinformatics, Peking University, Beijing.
- South Korea: http://kr.expasy.org/ at the Yonsei Proteome Research Center.
- Taiwan: http://tw.expasy.org/ at the National Health Research Institutes (NHRI), Taipei.
- United States: http://us.expasy.org/ at the North Carolina Supercomputing Center (NCSC).
| CONCLUSIONS |
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The team developing ExPASy is committed to bringing to its users top quality information services in the field of proteomics. We hope that in the next years we will be able to add many new features to those that are already available.
We strongly encourage users and providers of related web sites to link to ExPASy. Detailed documentation of how to create html links to the different services of ExPASy is available at http://www.expasy.org/expasy_urls.html.
To keep track of new developments on ExPASy, do not forget to subscribe to Swiss-Flash (http://www.expasy.org/swiss-flash/), a service that allows users to automatically obtain email bulletins that report new and updated ExPASy features.
| ACKNOWLEDGEMENTS |
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Finally, we want to thank all the users of ExPASy who, over the years, have sent us feedback that has led to the improvement of existing services and to the development of new ones.
| REFERENCES |
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S. Porcellini, L. Alberici, F. Gubinelli, R. Lupo, C. Olgiati, G.-P. Rizzardi, and C. Bovolenta The F12-Vif derivative Chim3 inhibits HIV-1 replication in CD4+ T lymphocytes and CD34+-derived macrophages by blocking HIV-1 DNA integration Blood, April 9, 2009; 113(15): 3443 - 3452. [Abstract] [Full Text] [PDF] |
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G. Perez, J. Pangilinan, A. G. Pisabarro, and L. Ramirez Telomere Organization in the Ligninolytic Basidiomycete Pleurotus ostreatus Appl. Envir. Microbiol., March 1, 2009; 75(5): 1427 - 1436. [Abstract] [Full Text] [PDF] |
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K. E. Hung, V. Faca, K. Song, D. A. Sarracino, L. G. Richard, B. Krastins, S. Forrester, A. Porter, A. Kunin, U. Mahmood, et al. Comprehensive Proteome Analysis of an Apc Mouse Model Uncovers Proteins Associated with Intestinal Tumorigenesis Cancer Prevention Research, March 1, 2009; 2(3): 224 - 233. [Abstract] [Full Text] [PDF] |
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W. C. Lima, A. M. Varani, and C. F.M. Menck NAD Biosynthesis Evolution in Bacteria: Lateral Gene Transfer of Kynurenine Pathway in Xanthomonadales and Flavobacteriales Mol. Biol. Evol., February 1, 2009; 26(2): 399 - 406. [Abstract] [Full Text] [PDF] |
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C. Vincke, R. Loris, D. Saerens, S. Martinez-Rodriguez, S. Muyldermans, and K. Conrath General Strategy to Humanize a Camelid Single-domain Antibody and Identification of a Universal Humanized Nanobody Scaffold J. Biol. Chem., January 30, 2009; 284(5): 3273 - 3284. [Abstract] [Full Text] [PDF] |
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J. Klein, R. Munch, I. Biegler, I. Haddad, I. Retter, and D. Jahn Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform 'Open Genome Resource' (OGeR) Nucleic Acids Res., January 1, 2009; 37(suppl_1): D494 - D498. [Abstract] [Full Text] [PDF] |
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K.-R. Chung and H.-L. Liao Determination of a transcriptional regulator-like gene involved in biosynthesis of elsinochrome phytotoxin by the citrus scab fungus, Elsinoe fawcettii Microbiology, November 1, 2008; 154(11): 3556 - 3566. [Abstract] [Full Text] [PDF] |
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M. Akif, G. Khare, A. K. Tyagi, S. C. Mande, and A. A. Sardesai Functional Studies of Multiple Thioredoxins from Mycobacterium tuberculosis J. Bacteriol., November 1, 2008; 190(21): 7087 - 7095. [Abstract] [Full Text] [PDF] |
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M. Skiba, T. C. Mettenleiter, and A. Karger Quantitative Whole-Cell Proteome Analysis of Pseudorabies Virus-Infected Cells J. Virol., October 1, 2008; 82(19): 9689 - 9699. [Abstract] [Full Text] [PDF] |
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C.A. Gifford, A.M. Assiri, M.C. Satterfield, T.E. Spencer, and T.L. Ott Receptor Transporter Protein 4 (RTP4) in Endometrium, Ovary, and Peripheral Blood Leukocytes of Pregnant and Cyclic Ewes Biol Reprod, September 1, 2008; 79(3): 518 - 524. [Abstract] [Full Text] [PDF] |
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C. Bauvois, L. Jacquamet, A. L. Huston, F. Borel, G. Feller, and J.-L. Ferrer Crystal Structure of the Cold-active Aminopeptidase from Colwellia psychrerythraea, a Close Structural Homologue of the Human Bifunctional Leukotriene A4 Hydrolase J. Biol. Chem., August 22, 2008; 283(34): 23315 - 23325. [Abstract] [Full Text] [PDF] |
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A. X. Tran, M. S. Trent, and C. Whitfield The LptA Protein of Escherichia coli Is a Periplasmic Lipid A-binding Protein Involved in the Lipopolysaccharide Export Pathway J. Biol. Chem., July 18, 2008; 283(29): 20342 - 20349. [Abstract] [Full Text] [PDF] |
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M. Moroni, R. Vijayan, A. Carbone, R. Zwart, P. C. Biggin, and I. Bermudez Non-Agonist-Binding Subunit Interfaces Confer Distinct Functional Signatures to the Alternate Stoichiometries of the {alpha}4{beta}2 Nicotinic Receptor: An {alpha}4-{alpha}4 Interface Is Required for Zn2+ Potentiation J. Neurosci., July 2, 2008; 28(27): 6884 - 6894. [Abstract] [Full Text] [PDF] |
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A. H. Davis, N. V. Guseva, B. L. Ball, and J. W. Heusel Characterization of Murine Cytomegalovirus m157 from Infected Cells and Identification of Critical Residues Mediating Recognition by the NK Cell Receptor Ly49H J. Immunol., July 1, 2008; 181(1): 265 - 275. [Abstract] [Full Text] [PDF] |
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E. M. Pasini, M. Kirkegaard, D. Salerno, P. Mortensen, M. Mann, and A. W. Thomas Deep Coverage Mouse Red Blood Cell Proteome: A First Comparison with the Human Red Blood Cell Mol. Cell. Proteomics, July 1, 2008; 7(7): 1317 - 1330. [Abstract] [Full Text] [PDF] |
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F. Lemoine, B. Labedan, and C. Froidevaux GenoQuery: a new querying module for functional annotation in a genomic warehouse Bioinformatics, July 1, 2008; 24(13): i322 - i329. [Abstract] [Full Text] [PDF] |
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I. M. Overton, C. A. J. van Niekerk, L. G. Carter, A. Dawson, D. M. A. Martin, S. Cameron, S. A. McMahon, M. F. White, W. N. Hunter, J. H. Naismith, et al. TarO: a target optimisation system for structural biology Nucleic Acids Res., July 1, 2008; 36(suppl_2): W190 - W196. [Abstract] [Full Text] [PDF] |
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L.-C. Tranchevent, R. Barriot, S. Yu, S. Van Vooren, P. Van Loo, B. Coessens, B. De Moor, S. Aerts, and Y. Moreau ENDEAVOUR update: a web resource for gene prioritization in multiple species Nucleic Acids Res., July 1, 2008; 36(suppl_2): W377 - W384. [Abstract] [Full Text] [PDF] |
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J. L. Lustgarten, C. Kimmel, H. Ryberg, and W. Hogan EPO-KB: a searchable knowledge base of biomarker to protein links Bioinformatics, June 1, 2008; 24(11): 1418 - 1419. [Abstract] [Full Text] [PDF] |
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O. A. Bazirgan and R. Y. Hampton Cue1p Is an Activator of Ubc7p E2 Activity in Vitro and in Vivo J. Biol. Chem., May 9, 2008; 283(19): 12797 - 12810. [Abstract] [Full Text] [PDF] |
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C. K. Tipsmark, P. Kiilerich, T. O. Nilsen, L. O. E. Ebbesson, S. O. Stefansson, and S. S. Madsen Branchial expression patterns of claudin isoforms in Atlantic salmon during seawater acclimation and smoltification Am J Physiol Regulatory Integrative Comp Physiol, May 1, 2008; 294(5): R1563 - R1574. [Abstract] [Full Text] [PDF] |
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C. K. Tipsmark Identification of FXYD protein genes in a teleost: tissue-specific expression and response to salinity change Am J Physiol Regulatory Integrative Comp Physiol, April 1, 2008; 294(4): R1367 - R1378. [Abstract] [Full Text] [PDF] |
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L. J. G. Robertson, L. L. David, M. A. Riviere, P. A. Wilmarth, M. S. Muir, and J. D. Morton Susceptibility of Ovine Lens Crystallins to Proteolytic Cleavage during Formation of Hereditary Cataract Invest. Ophthalmol. Vis. Sci., March 1, 2008; 49(3): 1016 - 1022. [Abstract] [Full Text] [PDF] |
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P. Vuong, D. Bennion, J. Mantei, D. Frost, and R. Misra Analysis of YfgL and YaeT Interactions through Bioinformatics, Mutagenesis, and Biochemistry J. Bacteriol., March 1, 2008; 190(5): 1507 - 1517. [Abstract] [Full Text] [PDF] |
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J. Castillo, B. Castellana, L. Acerete, J. V Planas, F. W Goetz, S. Mackenzie, and L. Tort Stress-induced regulation of steroidogenic acute regulatory protein expression in head kidney of Gilthead seabream (Sparus aurata) J. Endocrinol., February 1, 2008; 196(2): 313 - 322. [Abstract] [Full Text] [PDF] |
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C. Borghouts, C. Kunz, N. Delis, and B. Groner Monomeric Recombinant Peptide Aptamers Are Required for Efficient Intracellular Uptake and Target Inhibition Mol. Cancer Res., February 1, 2008; 6(2): 267 - 281. [Abstract] [Full Text] [PDF] |
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J. Piontek, L. Winkler, H. Wolburg, S. L. Muller, N. Zuleger, C. Piehl, B. Wiesner, G. Krause, and I. E. Blasig Formation of tight junction: determinants of homophilic interaction between classic claudins FASEB J, January 1, 2008; 22(1): 146 - 158. [Abstract] [Full Text] [PDF] |
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K. B. Gromadski, T. Schummer, A. Stromgaard, C. R. Knudsen, T. G. Kinzy, and M. V. Rodnina Kinetics of the Interactions between Yeast Elongation Factors 1A and 1B{alpha}, Guanine Nucleotides, and Aminoacyl-tRNA J. Biol. Chem., December 7, 2007; 282(49): 35629 - 35637. [Abstract] [Full Text] [PDF] |
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K. A. Swanson, D. D. Crane, and H. D. Caldwell Chlamydia trachomatis Species-Specific Induction of Ezrin Tyrosine Phosphorylation Functions in Pathogen Entry Infect. Immun., December 1, 2007; 75(12): 5669 - 5677. [Abstract] [Full Text] [PDF] |
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H. Wang, Y.-C. Liaw, D. Stone, O. Kalyuzhniy, I. Amiraslanov, S. Tuve, C. L. M. J. Verlinde, D. Shayakhmetov, T. Stehle, S. Roffler, et al. Identification of CD46 Binding Sites within the Adenovirus Serotype 35 Fiber Knob J. Virol., December 1, 2007; 81(23): 12785 - 12792. [Abstract] [Full Text] [PDF] |
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R. K. F. Beran, V. Serebrov, and A. M. Pyle The Serine Protease Domain of Hepatitis C Viral NS3 Activates RNA Helicase Activity by Promoting the Binding of RNA Substrate J. Biol. Chem., November 30, 2007; 282(48): 34913 - 34920. [Abstract] [Full Text] [PDF] |
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P. Nilsson, N. Henriksson, A. Niedzwiecka, N. A. A. Balatsos, K. Kokkoris, J. Eriksson, and A. Virtanen A Multifunctional RNA Recognition Motif in Poly(A)-specific Ribonuclease with Cap and Poly(A) Binding Properties J. Biol. Chem., November 9, 2007; 282(45): 32902 - 32911. [Abstract] [Full Text] [PDF] |
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M. Kato, S. Khan, E. d'Aniello, K. J. McDonald, and D. N. J. Hart The Novel Endocytic and Phagocytic C-Type Lectin Receptor DCL-1/CD302 on Macrophages Is Colocalized with F-Actin, Suggesting a Role in Cell Adhesion and Migration J. Immunol., November 1, 2007; 179(9): 6052 - 6063. [Abstract] [Full Text] [PDF] |
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R. J. Rojas, M. E. Yohe, S. Gershburg, T. Kawano, T. Kozasa, and J. Sondek G{alpha}q Directly Activates p63RhoGEF and Trio via a Conserved Extension of the Dbl Homology-associated Pleckstrin Homology Domain J. Biol. Chem., October 5, 2007; 282(40): 29201 - 29210. [Abstract] [Full Text] [PDF] |
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P. M. Swe, N. C. K. Heng, Y.-T. Ting, H. J. Baird, A. Carne, A. Tauch, J. R. Tagg, and R. W. Jack ef1097 and ypkK encode enterococcin V583 and corynicin JK, members of a new family of antimicrobial proteins (bacteriocins) with modular structure from Gram-positive bacteria Microbiology, October 1, 2007; 153(10): 3218 - 3227. [Abstract] [Full Text] [PDF] |
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P. Smialowski, A. J. Martin-Galiano, A. Mikolajka, T. Girschick, T. A. Holak, and D. Frishman Protein solubility: sequence based prediction and experimental verification Bioinformatics, October 1, 2007; 23(19): 2536 - 2542. [Abstract] [Full Text] [PDF] |
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A. P. Bussink, D. Speijer, J. M. F. G. Aerts, and R. G. Boot Evolution of Mammalian Chitinase(-Like) Members of Family 18 Glycosyl Hydrolases Genetics, October 1, 2007; 177(2): 959 - 970. [Abstract] [Full Text] [PDF] |
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S. P. Lad, G. Yang, D. A. Scott, G. Wang, P. Nair, J. Mathison, V. S. Reddy, and E. Li Chlamydial CT441 Is a PDZ Domain-Containing Tail-Specific Protease That Interferes with the NF-{kappa}B Pathway of Immune Response J. Bacteriol., September 15, 2007; 189(18): 6619 - 6625. [Abstract] [Full Text] [PDF] |
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A. V. Korennykh, C. C. Correll, and J. A. Piccirilli Evidence for the importance of electrostatics in the function of two distinct families of ribosome inactivating toxins RNA, September 1, 2007; 13(9): 1391 - 1396. [Abstract] [Full Text] [PDF] |
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L. C. Kudo, S. L. Karsten, J. Chen, P. Levitt, and D. H. Geschwind Genetic Analysis of Anterior Posterior Expression Gradients in the Developing Mammalian Forebrain Cereb Cortex, September 1, 2007; 17(9): 2108 - 2122. [Abstract] [Full Text] [PDF] |
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B. L. Yaspan, J. P. Breyer, Q. Cai, Q. Dai, J. B. Elmore, I. Amundson, K. M. Bradley, X.-O. Shu, Y.-T. Gao, W. D. Dupont, et al. Haplotype Analysis of CYP11A1 Identifies Promoter Variants Associated with Breast Cancer Risk Cancer Res., June 15, 2007; 67(12): 5673 - 5682. [Abstract] [Full Text] [PDF] |
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O. Perera, T. B. Green, S. M. Stevens Jr., S. White, and J. J. Becnel Proteins Associated with Culex nigripalpus Nucleopolyhedrovirus Occluded Virions J. Virol., May 1, 2007; 81(9): 4585 - 4590. [Abstract] [Full Text] [PDF] |
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X.-S. Zhang, R. Garcia-Contreras, and T. K. Wood YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity J. Bacteriol., April 15, 2007; 189(8): 3051 - 3062. [Abstract] [Full Text] [PDF] |
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C. Guillaume, P. Delobel, J.-M. Sablayrolles, and B. Blondin Molecular Basis of Fructose Utilization by the Wine Yeast Saccharomyces cerevisiae: a Mutated HXT3 Allele Enhances Fructose Fermentation Appl. Envir. Microbiol., April 15, 2007; 73(8): 2432 - 2439. [Abstract] [Full Text] [PDF] |
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G. Seibold, S. Dempf, J. Schreiner, and B. J. Eikmanns Glycogen formation in Corynebacterium glutamicum and role of ADP-glucose pyrophosphorylase Microbiology, April 1, 2007; 153(4): 1275 - 1285. [Abstract] [Full Text] [PDF] |
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J. M. Pagano, B. M. Farley, L. M. McCoig, and S. P. Ryder Molecular Basis of RNA Recognition by the Embryonic Polarity Determinant MEX-5 J. Biol. Chem., March 23, 2007; 282(12): 8883 - 8894. [Abstract] [Full Text] [PDF] |
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E. M. Smolock, T. Wang, J. K. Nolt, and R. S. Moreland siRNA knock down of casein kinase 2 increases force and cross-bridge cycling rates in vascular smooth muscle Am J Physiol Cell Physiol, February 1, 2007; 292(2): C876 - C885. [Abstract] [Full Text] [PDF] |
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K. Michael, B. G. Klupp, A. Karger, and T. C. Mettenleiter Efficient Incorporation of Tegument Proteins pUL46, pUL49, and pUS3 into Pseudorabies Virus Particles Depends on the Presence of pUL21 J. Virol., January 15, 2007; 81(2): 1048 - 1051. [Abstract] [Full Text] [PDF] |
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C. K. Taylor, D. D. Smith, M. Hulce, and P. W. Abel Pharmacological Characterization of Novel {alpha}-Calcitonin Gene-Related Peptide (CGRP) Receptor Peptide Antagonists That Are Selective for Human CGRP Receptors J. Pharmacol. Exp. Ther., November 1, 2006; 319(2): 749 - 757. [Abstract] [Full Text] [PDF] |
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J. Gioia, X. Qin, H. Jiang, K. Clinkenbeard, R. Lo, Y. Liu, G. E. Fox, S. Yerrapragada, M. P. McLeod, T. Z. McNeill, et al. The Genome Sequence of Mannheimia haemolytica A1: Insights into Virulence, Natural Competence, and Pasteurellaceae Phylogeny. J. Bacteriol., October 1, 2006; 188(20): 7257 - 7266. [Abstract] [Full Text] [PDF] |
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P. Knechtle, J. Wendland, and P. Philippsen The SH3/PH Domain Protein AgBoi1/2 Collaborates with the Rho-Type GTPase AgRho3 To Prevent Nonpolar Growth at Hyphal Tips of Ashbya gossypii Eukaryot. Cell, October 1, 2006; 5(10): 1635 - 1647. [Abstract] [Full Text] [PDF] |
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J. Van Durme, F. Horn, S. Costagliola, G. Vriend, and G. Vassart GRIS: Glycoprotein-Hormone Receptor Information System Mol. Endocrinol., September 1, 2006; 20(9): 2247 - 2255. [Abstract] [Full Text] [PDF] |
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E. M. Pasini, M. Kirkegaard, P. Mortensen, H. U. Lutz, A. W. Thomas, and M. Mann In-depth analysis of the membrane and cytosolic proteome of red blood cells Blood, August 1, 2006; 108(3): 791 - 801. [Abstract] [Full Text] [PDF] |
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S. R. Escasa, H. A. M. Lauzon, A. C. Mathur, P. J. Krell, and B. M. Arif Sequence analysis of the Choristoneura occidentalis granulovirus genome J. Gen. Virol., July 1, 2006; 87(7): 1917 - 1933. [Abstract] [Full Text] [PDF] |
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J. Dundas, Z. Ouyang, J. Tseng, A. Binkowski, Y. Turpaz, and J. Liang CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W116 - W118. [Abstract] [Full Text] [PDF] |
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E. de Castro, C. J. A. Sigrist, A. Gattiker, V. Bulliard, P. S. Langendijk-Genevaux, E. Gasteiger, A. Bairoch, and N. Hulo ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W362 - W365. [Abstract] [Full Text] [PDF] |
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Y. Ponty, M. Termier, and A. Denise GenRGenS: software for generating random genomic sequences and structures Bioinformatics, June 15, 2006; 22(12): 1534 - 1535. [Abstract] [Full Text] [PDF] |
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S. Verma, V. Bednar, A. Blount, and B. G. Hogue Identification of Functionally Important Negatively Charged Residues in the Carboxy End of Mouse Hepatitis Coronavirus A59 Nucleocapsid Protein J. Virol., May 1, 2006; 80(9): 4344 - 4355. [Abstract] [Full Text] [PDF] |
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B. A. McDaniel, F. J. Grundy, V. P. Kurlekar, J. Tomsic, and T. M. Henkin Identification of a Mutation in the Bacillus subtilis S-Adenosylmethionine Synthetase Gene That Results in Derepression of S-Box Gene Expression. J. Bacteriol., May 1, 2006; 188(10): 3674 - 3681. [Abstract] [Full Text] [PDF] |
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P. Roccabianca, M. Rondena, S. Paltrinieri, V. Pocacqua, P. Scarpa, S. Faverzani, E. Scanziani, and M. Caniatti Multiple Endocrine Neoplasia Type-I-like Syndrome in Two Cats Vet. Pathol., May 1, 2006; 43(3): 345 - 352. [Abstract] [Full Text] [PDF] |
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J.F. Sorensen and O. Sibbesen Mapping of residues involved in the interaction between the Bacillus subtilis xylanase A and proteinaceous wheat xylanase inhibitors Protein Eng. Des. Sel., May 1, 2006; 19(5): 205 - 210. [Abstract] [Full Text] [PDF] |
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P. C. Hanington, D. R. Barreda, and M. Belosevic A Novel Hematopoietic Granulin Induces Proliferation of Goldfish (Carassius auratus L.) Macrophages J. Biol. Chem., April 14, 2006; 281(15): 9963 - 9970. [Abstract] [Full Text] [PDF] |
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L. A. Cox, M. J. Nijland, J. S. Gilbert, N. E. Schlabritz-Loutsevitch, G. B. Hubbard, T. J. McDonald, R. E. Shade, and P. W. Nathanielsz Effect of 30 per cent maternal nutrient restriction from 0.16 to 0.5 gestation on fetal baboon kidney gene expression J. Physiol., April 1, 2006; 572(1): 67 - 85. [Abstract] [Full Text] [PDF] |
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E. Brombacher, A. Baratto, C. Dorel, and P. Landini Gene Expression Regulation by the Curli Activator CsgD Protein: Modulation of Cellulose Biosynthesis and Control of Negative Determinants for Microbial Adhesion J. Bacteriol., March 15, 2006; 188(6): 2027 - 2037. [Abstract] [Full Text] [PDF] |
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A. P. R. Zabell, A. D. Schroff Jr., B. E. Bain, R. L. Van Etten, O. Wiest, and C. V. Stauffacher Crystal Structure of the Human B-form Low Molecular Weight Phosphotyrosyl Phosphatase at 1.6-A Resolution J. Biol. Chem., March 10, 2006; 281(10): 6520 - 6527. [Abstract] [Full Text] [PDF] |
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G. Beyene, C. H. Foyer, and K. J. Kunert Two new cysteine proteinases with specific expression patterns in mature and senescent tobacco (Nicotiana tabacum L.) leaves J. Exp. Bot., March 1, 2006; 57(6): 1431 - 1443. [Abstract] [Full Text] [PDF] |
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M. S. Macauley, W. J. Errington, M. Scharpf, C. D. Mackereth, A. G. Blaszczak, B. J. Graves, and L. P. McIntosh Beads-on-a-String, Characterization of Ets-1 Sumoylated within Its Flexible N-terminal Sequence J. Biol. Chem., February 17, 2006; 281(7): 4164 - 4172. [Abstract] [Full Text] [PDF] |
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E. Moe, I. Leiros, A. O. Smalas, and S. McSweeney The Crystal Structure of Mismatch-specific Uracil-DNA Glycosylase (MUG) from Deinococcus radiodurans Reveals a Novel Catalytic Residue and Broad Substrate Specificity J. Biol. Chem., January 6, 2006; 281(1): 569 - 577. [Abstract] [Full Text] [PDF] |
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E. J. Summer, C. F. Gonzalez, M. Bomer, T. Carlile, A. Embry, A. M. Kucherka, J. Lee, L. Mebane, W. C. Morrison, L. Mark, et al. Divergence and Mosaicism among Virulent Soil Phages of the Burkholderia cepacia Complex J. Bacteriol., January 1, 2006; 188(1): 255 - 268. [Abstract] [Full Text] [PDF] |
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D. N. Eidhin, A. W. Ryan, R. M. Doyle, J. B. Walsh, and D. Kelleher Sequence and phylogenetic analysis of the gene for surface layer protein, slpA, from 14 PCR ribotypes of Clostridium difficile J. Med. Microbiol., January 1, 2006; 55(1): 69 - 83. [Abstract] [Full Text] [PDF] |
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C. L. ZHENG, Y.-S. KWON, H.-R. LI, K. ZHANG, G. COUTINHO-MANSFIELD, C. YANG, T. M. NAIR, M. GRIBSKOV, and X.-D. FU MAASE: An alternative splicing database designed for supporting splicing microarray applications RNA, December 1, 2005; 11(12): 1767 - 1776. [Abstract] [Full Text] [PDF] |
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K. Preiter, D. M. Brooks, A. Penaloza-Vazquez, A. Sreedharan, C. L. Bender, and B. N. Kunkel Novel Virulence Gene of Pseudomonas syringae pv. tomato Strain DC3000 J. Bacteriol., November 15, 2005; 187(22): 7805 - 7814. [Abstract] [Full Text] [PDF] |
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D. O. d. O. Lucana, P. Zou, M. Nierhaus, and H. Schrempf Identification of a novel two-component system SenS/SenR modulating the production of the catalase-peroxidase CpeB and the haem-binding protein HbpS in Streptomyces reticuli Microbiology, November 1, 2005; 151(11): 3603 - 3614. [Abstract] [Full Text] [PDF] |
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V. Aspehaug, A. B. Mikalsen, M. Snow, E. Biering, and S. Villoing Characterization of the Infectious Salmon Anemia Virus Fusion Protein J. Virol., October 1, 2005; 79(19): 12544 - 12553. [Abstract] [Full Text] [PDF] |
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M. Suarez, M. Haenni, S. Canarelli, F. Fisch, P. Chodanowski, C. Servis, O. Michielin, R. Freitag, P. Moreillon, and N. Mermod Structure-Function Characterization and Optimization of a Plant-Derived Antibacterial Peptide Antimicrob. Agents Chemother., September 1, 2005; 49(9): 3847 - 3857. [Abstract] [Full Text] [PDF] |
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M. Kontou, L. Govindasamy, H.-J. Nam, N. Bryant, A. L. Llamas-Saiz, C. Foces-Foces, E. Hernando, M.-P. Rubio, R. McKenna, J. M. Almendral, et al. Structural Determinants of Tissue Tropism and In Vivo Pathogenicity for the Parvovirus Minute Virus of Mice J. Virol., September 1, 2005; 79(17): 10931 - 10943. [Abstract] [Full Text] [PDF] |
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Z. Wilczynska, K. Happle, A. Muller-Taubenberger, C. Schlatterer, D. Malchow, and P. R. Fisher Release of Ca2+ from the Endoplasmic Reticulum Contributes to Ca2+ Signaling in Dictyostelium discoideum Eukaryot. Cell, September 1, 2005; 4(9): 1513 - 1525. [Abstract] [Full Text] [PDF] |
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F. Lu, S. Keles, S. J. Wright, and G. Wahba Framework for kernel regularization with application to protein clustering PNAS, August 30, 2005; 102(35): 12332 - 12337. [Abstract] [Full Text] [PDF] |
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A. Atanassova and D. B. Zamble Escherichia coli HypA Is a Zinc Metalloprotein with a Weak Affinity for Nickel J. Bacteriol., July 15, 2005; 187(14): 4689 - 4697. [Abstract] [Full Text] [PDF] |
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D. Villarreal, P. Nirde, M. Hide, C. Barnabe, and M. Tibayrenc Differential Gene Expression in Benznidazole-Resistant Trypanosoma cruzi Parasites Antimicrob. Agents Chemother., July 1, 2005; 49(7): 2701 - 2709. [Abstract] [Full Text] [PDF] |
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S.-C. Wu and S.-L. Wong Engineering Soluble Monomeric Streptavidin with Reversible Biotin Binding Capability J. Biol. Chem., June 17, 2005; 280(24): 23225 - 23231. [Abstract] [Full Text] [PDF] |
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J. Spaethe and A. D. Briscoe Molecular characterization and expression of the UV opsin in bumblebees: three ommatidial subtypes in the retina and a new photoreceptor organ in the lamina J. Exp. Biol., June 15, 2005; 208(12): 2347 - 2361. [Abstract] [Full Text] [PDF] |
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T. M. Onorato, S. Chakraborty, and D. Haldar Phosphorylation of Rat Liver Mitochondrial Glycerol-3-phosphate Acyltransferase by Casein Kinase 2 J. Biol. Chem., May 20, 2005; 280(20): 19527 - 19534. [Abstract] [Full Text] [PDF] |
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V. Wiwanitkit Study on the Phylogenetic Treeof Human Platelet Glycoproteins Clinical and Applied Thrombosis/Hemostasis, April 1, 2005; 11(2): 219 - 221. [Abstract] [PDF] |
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