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http://topdb.enzim.hu

Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data.

Proper citation: Topology Data Bank of Transmembrane Proteins (RRID:SCR_007964) Copy   

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http://mips.gsf.de/proj/ppi/

The MIPS mammalian protein-protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published experimental evidence that has been processed by human expert curators. It is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions. To suit different users needs we provide a variety of interfaces to search the database: -Expert interface Simple but powerful boolean query language. -PPI search form Easy to use PPI search -Protein search Just find proteins of interest in the database Sponsors: This work is funded by a grant from the German Federal Ministry of Education and Research.

Proper citation: MIPS Mammalian Protein-Protein Interaction Database (RRID:SCR_008207) Copy   

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http://mips.helmholtz-muenchen.de/genre/proj/mpcdb/

A database of manually annotated mammalian protein complexes. To obtain a high-quality dataset, information was extracted from individual experiments described in the scientific literature. Data from high-throughput experiments was not included.

Proper citation: Mammalian Protein Complex Data Base (RRID:SCR_008209) Copy   

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http://locustdb.genomics.org.cn/

The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects. Its transcriptomic data provide invaluable information for molecular entomology study of the insect and pave a way for comparative studies of other medically, agronomically, and ecologically relevant insects. This first transcriptomic database of the locust (LocustDB) has been developed, building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. It currently hosts 45,474 high quality EST sequences from the locust, which were assembled into 12,161 unigenes. This database contains original sequence data, including homologous/orthologous sequences, functional annotations, pathway analysis, and codon usage, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. LocustDB also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. It starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporation of in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies.

Proper citation: Migratory Locust EST Database (RRID:SCR_008201) Copy   

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http://www.ebi.ac.uk/asd/altsplice/index.html

AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations. This data is being integrated with other data that is generated by other members of the ASD consortium. The ASD project will provide the following in its three year duration: -human curated database of alternative spliced genes and their properties -a computer generated database of alternatively spliced genes and their properties -the integration of the above and newly found knowledge in a user-friendly interface and research workbench for both bioinformaticists and biologists -DNA chips that are based on the data in the above databases -the DNA chips will be used to test against predisposition for and diagnoses of human diseases ASD aims to analyse this mechanism on a genome-wide scale by creating a database that contains all alternatively spliced exons from human, and other model species. Disease causing mutations seem to induce aberrations in the process of splicing and its regulation. The ASD consortium will develop a DNA microarray (chip) that contains cDNAs of all the splicing regulatory proteins and their isoforms, as well as a chip that contains a number of disease relevant genes. We will concentrate on three models of disease (breast cancer, FTDP-17, male infertility) in which a connection between mis-splicing and a pathological state has been observed. Finally, these chips will be developed as demonstrative kits to detect predisposition for and diagnosis of such diseases. Categories: Nucleotide Sequences: Gene Structure, Introns and Exons, & Splice Sites Databases

Proper citation: AltSplice Database of Alternative Spliced Events (RRID:SCR_008162) Copy   

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http://dimer.tamu.edu/doodle/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Doodle is a database that was developed to store and distribute information about the protein oligomerization domains that are encoded by various genomes. The protein oligomerization domains described here were found using the lambda repressor fusion system. Doodle uses a schema that is based on EnsEMBL, while also utilizing bioperl modules to both store and retrieve data. The frontend was developed entirely in perl, while the backend utilizes MySQL. GMOD was used to develop the genomic view.

Proper citation: Database of oligomerization domains from lambda experiments (RRID:SCR_008107) Copy   

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http://www.schematikon.org/Nh3D.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. It is a dataset of structurally dissimilar proteins. This dataset has been compiled by selecting well resolved representatives from the Topology level of the CATH database which hierarchically classifies all protein structures. These have been been pruned to remove: i) domains that may contain homologous elements (by pairwise sequence comparison and structural superposition of aligned residues) ii) internal duplications (by repeat detection) iii) regions with high B-Factor The statistical analysis of protein structures requires datasets in which structural features can be considered independently distributed, i.e. not related through common ancestry, and that fulfill minimal requirements regarding the experimental quality of the structures it contains. However, non-redundant datasets based on sequence similarity invariably contain distantly related homologues. Here a reference dataset of non-homologous protein domains is provided, assuming that structural dissimilarity at the topology level is incompatible with recognizable common ancestry. It contains the best refined representatives of each Topology level, validates structural dissimilarity and removes internally duplicated fragments. The compilation of Nh3D is fully scripted. The current Nh3D list contains 570 domains with a total of 90780 residues. It covers more than 70% of folds at the Topology level of the CATH database and represents more than 90% of the structures in the PDB that have been classified by CATH. Even though all protein pairs are structurally dissimilar, some pairwise sequence identities after global alignment are greater than 30%. Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB.

Proper citation: Nh3D: A Reference Dataset of Structures of Non-homologous Proteins (RRID:SCR_008212) Copy   

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http://jbirc.jbic.or.jp/hinv/ppi/

The PPI view displays H-InvDB human protein-protein interaction (PPI) information. It is constructed by assigning interaction data to H-InvDB proteins which were originally predicted from transcriptional products generated by the H-Invitational project. The PPI view is now providing 32,198 human PPIs comprised of 9,268 H-InvDB proteins. H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. Sponsors: This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program.

Proper citation: H-Invitational Database: Protein-Protein Interaction Viewer (RRID:SCR_008054) Copy   

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http://ligand-expo.rutgers.edu/

An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components.

Proper citation: Ligand Expo (RRID:SCR_006636) Copy   

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http://www.dpvweb.net/

DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. The start and end positions of each feature (gene, non-translated region and the like) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the website) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses. The public sequence databases contain vast amounts of data on virus genomes but accessing and comparing the data, except for relatively small sets of related viruses can be very time consuming. The procedure is made difficult because some of the sequences on these databases are incorrectly named, poorly annotated or redundant. The NCBI Reference Sequence project (1) provides a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA) and protein products, for major research organisms. This now includes curated information for a single sequence of each fully sequenced virus species. While this is a welcome development, it can only deal with complete sequences. An important feature of DPV is the opportunity to access genes (and other features) of multiple sequences quickly and accurately. Thus, for example, it is easy to obtain the nucleotide or amino acid sequences of all the available accessions of the coat protein gene of a given virus species or for a group of viruses. To increase its usefulness further, DPVweb also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA (ssDNA) genome. Sponsors: This site is supported by the Association of Applied Biologists and the Zhejiang Academy of Agricultural Sciences, Hangzhou, People''s Republic of China.

Proper citation: Descriptions of Plant Viruses (RRID:SCR_006656) Copy   

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http://ardb.cbcb.umd.edu

The goals of Antibiotic Resistance Genes Database (ARGB) are to provide a centralized compendium of information on antibiotic resistance, to facilitate the consistent annotation of resistance information in newly sequenced organisms, and also to facilitate the identification and characterization of new genes. ARGB contains six types of database groups: - Resistance Type: This database contains information, such as resistance profile, mechanism, requirement, epidemiology for each type. - Resistance Gene: This database contains information, such as resistance profile, resistance type, requirement, protein and DNA sequence for each gene.This database only includes NON-REDUNDANT, NON-VECTOR, COMPLETE genes. - Antibiotic: This database contains information, such as producer, action mechanism, resistance type, for each gene. - Resistance Gene(NonRD): This database contains the same information as Resistance Gene. It does NOT include NON-REDUNDANT, NON-VECTOR genes, but includes INCOMPLETE genes. - Resistance Gene(ALL): This database contains the same information as Resistance Gene. It includes all REDUNDANT, VECTOR AND INCOMPLETE genes. - Resistance Species: This database contains resistance profile and corresponding resistance genes for each species. Furthermore, ARDB also contians three types BLAST database: - Resistance Genes Complete: Contains only NON-REDUNDANT, NON-VECTOR, COMPLETE genes sequences. - Resistance Genes Non-redundant: Contains NON-REDUNDANT, NON-VECTOR, COMPLETE, INCOMPLETE genes sequences. - Resistance Genes All: Contains all REDUNDANT, VECTOR, COMPLETE, INCOMPLETE genes sequences. Lastly, ARDB provides four types of Analytical tools: - Normal BLAST: This function allows an user to input a DNA or protein sequence, and find similar DNA (Nucleotide BLAST) or protein (Protein BLAST) sequences using blastn, blastp, blastx, tblastn, tblastx - RPS BLAST: A web RPSBLAST (RPS BLAST) interface is provided to align a query sequence against the Position Specific Scoring Matrix (PSSM) for each type. Normally, this will give the same annotation information as using regular BLAST mentioned above. - Multiple Sequences BLAST (Genome Annotation): This function allows an user to annotate multiple (less than 5000) query sequences in FASTA format. - Mutation Resistance Identification: This function allows an user to identify mutations that will cause potential antibiotic resistance, for 12 genes (16S rRNA, 23S rRNA, gyrA, gyrB, parC, parE, rpoB, katG, pncA, embB, folP, dfr). ������ :Sponsors: ARDB is funded by Uniformed Services University of the Health Sciences, administered by the Henry Jackson Foundation. :

Proper citation: Antibiotic Resistance Genes Database (RRID:SCR_007040) Copy   

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http://www.genoscope.cns.fr/externe/tetraodon/

The initial objective of Genoscope was to compare the genomic sequences of this fish to that of humans to help in the annotation of human genes and to estimate their number. This strategy is based on the common genetic heritage of the vertebrates: from one species of vertebrate to another, even for those as far apart as a fish and a mammal, the same genes are present for the most part. In the case of the compact genome of Tetraodon, this common complement of genes is contained in a genome eight times smaller than that of humans. Although the length of the exons is similar in these two species, the size of the introns and the intergenic sequences is greatly reduced in this fish. Furthermore, these regions, in contrast to the exons, have diverged completely since the separation of the lineages leading to humans and Tetraodon. The Exofish method, developed at Genoscope, exploits this contrast such that the conserved regions which can be identified by comparing genomic sequences of the two species, correspond only to coding regions. Using preliminary sequencing results of the genome of Tetraodon in the year 2000, Genoscope evaluated the number of human genes at about 30,000, whereas much higher estimations were current. The progress of the annotation of the human genome has since supported the Genoscope hypothesis, with values as low as 22,000 genes and a consensus of around 25,000 genes. The sequencing of the Tetraodon genome at a depth of about 8X, carried out as a collaboration between Genoscope and the Whitehead Institute Center for Genome Research (now the Broad Institute), was finished in 2002, with the production of an assembly covering 90 of the euchromatic region of the genome of the fish. This has permitted the application of Exofish at a larger scale in comparisons with the genome of humans, but also with those of the two other vertebrates sequenced at the time (Takifugu, a fish closely related to Tetraodon, and the mouse). The conserved regions detected in this way have been integrated into the annotation procedure, along with other resources (cDNA sequences from Tetraodon and ab initio predictions). Of the 28,000 genes annotated, some families were examined in detail: selenoproteins, and Type 1 cytokines and their receptors. The comparison of the proteome of Tetraodon with those of mammals has revealed some interesting differences, such as a major diversification of some hormone systems and of the collagen molecules in the fish. A search for transposable elements in the genomic sequences of Tetraodon has also revealed a high diversity (75 types), which contrasts with their scarcity; the small size of the Tetraodon genome is due to the low abundance of these elements, of which some appear to still be active. Another factor in the compactness of the Tetraodon genome, which has been confirmed by annotation, is the reduction in intron size, which approaches a lower limit of 50-60 bp, and which preferentially affects certain genes. The availability of the sequences from the genomes of humans and mice on one hand, and Takifugu and Tetraodon on the other, provide new opportunities for the study of vertebrate evolution. We have shown that the level of neutral evolution is higher in fish than in mammals. The protein sequences of fish also diverge more quickly than those of mammals. A key mechanism in evolution is gene duplication, which we have studied by taking advantage of the anchoring of the majority of the sequences from the assembly on the chromosomes. The result of this study speaks strongly in favor of a whole genome duplication event, very early in the line of ray-finned fish (Actinopterygians). An even stronger evidence came from synteny studies between the genomes of humans and Tetraodon. Using a high-resolution synteny map, we have reconstituted the genome of the vertebrate which predates this duplication - that is, the last common ancestor to all bony vertebrates (most of the vertebrates apart from cartilaginous fish and agnaths like lamprey). This ancestral karyotype contains 12 chromosomes, and the 21 Tetraodon chromosomes derive from it by the whole genome duplication and a surprisingly small number of interchromosomal rearrangements. On the contrary, exchanges between chromosomes have been much more frequent in the lineage that leads to humans. Sponsors: The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute.

Proper citation: Tetraodon Genome Browser (RRID:SCR_007079) Copy   

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http://www.molgen.de

The research of the group concentrates on the molecular biology of Gram-positive bacteria, with Bacillus subtilis and Lactococcus lactis as the main model organisms. A number of important (human) pathogens are also investigated: Bacillus cereus, Streptococcus pneumoniae and Enterococcus faecalis. The nature of the research is both fundamental and application-oriented. Transcript- and protein profiling by high-throughput technologies such as DNA microarrays and proteomics tools are being used. The very large data sets generated are analyzed by employing existing and novel bioinformatics tools. Major lines of research are in the field of functional genomics of these organisms, using systems- and synthetic biology approaches.

Proper citation: MolGen (RRID:SCR_005700) Copy   

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http://www.gene-regulation.com/pub/databases.html

In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers academic and non-profit organizations free access to reduced functionality versions of their products. TRANSFAC Professional provides gene regulation analysis solutions, offering the most comprehensive collection of eukaryotic gene regulation data. The professional paid subscription gives customers access to up-to-date data and tools not available in the free version. The public databases currently available for academic and non-profit organizations are: * TRANSFAC: contains data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. * TRANSPATH: provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signaling components.TRANSPATH focuses on signaling cascades that change the activities of transcription factors and thus alter the gene expression profile of a given cell. * PathoDB: is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. * S/MARt DB: presents data on scaffold or matrix attached regions (S/MARs) of eukaryotic genomes, as well as about the proteins that bind to them. S/MARs organize the chromatin in the form of functionally independent loop domains gained increasing support. Scaffold or Matrix Attached Regions (S/MARs) are genomic DNA sequences through which the chromatin is tightly attached to the proteinaceous scaffold of the nucleus. * TRANSCompel: is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signaling pathways. * PathoSign Public: is a database which collects information about defective cell signaling molecules causing human diseases. While constituting a useful data repository in itself, PathoSign is also aimed at being a foundational part of a platform for modeling human disease processes.

Proper citation: Gene Regulation Databases (RRID:SCR_008033) Copy   

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http://www.stanford.edu/group/nusselab/cgi-bin/wnt/

A resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year.

Proper citation: Wnt homepage (RRID:SCR_000662) Copy   

•   Source: SciCrunch Registry

http://www.bumc.bu.edu/cardiovascularproteomics/

The Cardiovascular Proteomics Center is a research center funded by the NIH/NHLBI to analyze and identify proteins that may be modified or created by oxidative stress. The CPC is developing and applying new proteomics methodology and instrumentation to the analysis of known proteins and those yet to be discovered.

Proper citation: Cardiovascular Proteomics Center (RRID:SCR_000603) Copy   

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http://cshprotocols.cshlp.org/cgi/collection/behavioral_assays

A bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format.

Proper citation: Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays (RRID:SCR_001697) Copy   

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http://molevol.cmima.csic.es/castresana/Gblocks_server.html

Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gblocks (RRID:SCR_015945) Copy   

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http://gps.biocuckoo.org/

Software that detects kinase-specific phosphorylation sites. GPS provides a platform able to perform its prediction based on a group-based phosphorylation scoring algorithm. It allows users to query multiple protein sequences through a batch prediction mode.

Proper citation: GPS (RRID:SCR_016374) Copy   

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http://silac.org/

Stable isotope labeling with amino acids in cell culture (SILAC) is a simple and straightforward approach for in vivo incorporation of a label into proteins for mass spectrometry (MS)-based quantitative proteomics. SILAC relies on metabolic incorporation of a given "light" or "heavy" form of the amino acid into the proteins. The method relies on the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, 13C, 15N). In an experiment, two cell populations are grown in culture media that are identical except that one of them contains a "light" and the other a "heavy" form of a particular amino acid (e.g. 12C and 13C labeled L-lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of this particular amino acid will be replaced by its isotope labeled analog. Since there is hardly any chemical difference between the labeled amino acid and the natural amino acid isotopes, the cells behave exactly like the control cell population grown in the presence of normal amino acid. It is efficient and reproducible as the incorporation of the isotope label is 100%. SILAC Applications: - Differential expression of proteins and identification of disease biomarkers - Cell signaling dynamics - Analysis of yeast pheromone signaling pathway - Identification of methylation sites - Identification of protease substrates - Study of protein complexes/protein interactions - Analysis of signaling pathways and effect of pharmacological inhibitors - Subcellular proteomics Sponsors: Supported in part by an NIH Roadmap grant Technology Center for Networks & Pathways of Lysine Modification.

Proper citation: Stable Isotope Labeling with Amino Acids in Cell Culture (RRID:SCR_001873) Copy   

•   Source: SciCrunch Registry