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THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of predicted specificity-determining residues in protein families. Predicted positions may have been used during evolution to change the function of proteins within a protein family. These positions are excellent targets for mutational studies and should lead to a better understading of protein function. SDR uses the PFAM database of protein domains for sequence alignments and domain definitions as well as the GPCR database for G-protein coupled receptors.

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• SciCrunch
• 17 years ago - by Anonymous

SCOPPI is a database of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions. Interfaces are classified according to the geometry of the domain associations and are annotated with various interaction characteristics. Screenshots of all interfaces are available. More than 4,000 distinct types of domain interfaces are collected from Protein Quaternary Structure Server and Protein Data Bank. Given a pair of interacting domains, we define face as the set of interacting residues in each single domain and the pair of interacting faces as an interface. We investigate how the geometry of interfaces relates to a network of interacting protein families, such as how many different binding orientations are possible between two families or whether a family uses distinct surfaces or the same surface when the family has diverse interaction partners from various families. We show there are, on average, 1.2-1.9 different types of interfaces between interacting domains and a significant number of family pairs associate in multiple orientations. In general, a family tends to use distinct faces for each partner when the family has diverse interaction partners. Each face is highly specific to its interaction partner and the binding orientation. The relative positions of interface residues are generally well conserved within the same type of interface even between remote homologs.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A candidate gene database for Spinocerebellar ataxia (SCA), which collected 3185 genes for 17 types of SCA. Those SCA subtypes that have known disease genes can be used as positive controls to optimize the parameters. The users may browse the candidate genes of a given SCA subtype by using the default parameters. The known disease genes were found to be the top three candidates using the default parameters. Alternatively, the users may score the candidate genes by changing the weight or the scores on the basis of their own working hypothesis.

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• SciCrunch
• 17 years ago - by Anonymous

SBASE is a database of protein domain sequences collected from the literature, from protein sequence databases and from genomic databases. The protein domains are defined by their sequence boundaries given by the publishing authors or in one of the primary sequence databases (Swiss-Prot, PIR, TREMBL etc.). Domain groups are included if they have well defined sequence boundaries, and if they can be distinguished from other sequences using a similarity search technique. The SBASE database uses a set theoretical approach for representing similarities, which in practical terms is extremely simple. Sequences are considered similar if they are members of a similarity group in which all or most sequences are similar to each other and less similar to other members of the database. Sequences that have an above threshold BLAST similarity score to at least one member of the group is called the neighbourhood of the group. The below sketch shows such a neighborhood; the similarities within the group (self-similarities) and those pointing to non-member neighbours (non-self similarities) are shown in different colours., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

The graduate program in Neuroscience is a multidisciplinary, interdepartmental program divided into three main areas: Cell and Molecular Neuroscience, Development and Regeneration, and Systems Neuroscience. Their research relates to many human diseases and disorders including fetal alcohol syndrome, spinal cord injury, degenerative retinal disease, Alzheimer''s disease, multiple sclerosis, cerebral palsy, and amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig''s disease.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 9, 2014. SARS-CoV RNA SSS DATABASE is a database of the predicted RNA secondary structural sequences of six SARS coronaviruse complete genomes. These structures were sequenced and submitted to GenBank by the separate sequencing and research groups from countries and areas, including Beijing, Hong Kong, Taiwan, USA, Canada, and Germany. The database provides the detailed information of all the possible hairpin loops, interior loops, bulge loops, multi-branched loops, double-stranded stems, and free unpaired nucleotides of RNA secondary structural sequences of six SARS isolates, BJ01(Accession: AY278488), CUHK-AG01 (Accession: AY345986), TWY (Accession: AP006561), Urbani (Accession: AY278741), TOR2 (Accession: AY274119), and Frankurt 1 (Accession: AY291315). . The ORIGIN sequences in the database are from the NCBI's GenBank.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The S4 database contains sequence alignments of domains in SCOP superfamilies. The aligned domains are selected using ASTRAL so that no two domains in the alignment have more than 40 percent identity and, moreover, they align all domains identified by ASTRAL as having less than 40 percent sequence identity. The alignments are generated using information from pairwise structural alignments of all domains in a given superfamily. These structural alignments generate residue equivalences and distances between residues, as well as an overall similarity of the two domains being compared (RMSD). This information is used to score individual the equivalences between residues. The scores are then integrated using a multiple sequence alignment program to generate the finished alignment. This database allows alignments to be retrieved in clustal format, or viewed in a web browser, with either structural or sequence features annotated. In addition, the statistics of structural diversity for each superfamily can be seen. The pairwise structural alignments were performed using the SAP program. The output of SAP was converted to a T-Coffee library so that the multiple sequence alignment T-Coffee could be use to compute the sequence alignments.

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• SciCrunch
• 17 years ago - by Anonymous

It collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. It covers the whole range from yeast to human. The SMAR table gives information on individual sequence elements of experimentally proven matrix binding activity. In release 2.3 it contains 500 entries. The sequences therein can be assigned to more than 150 genes from eukaryotic species ranging from yeast to human. The SMARbinder table contains 96 entries (release 2.3), but this figure does not reflect the number of independent S/MAR binding proteins. First of all, homologous factors from different species such as human and mouse SATB1 are given in different entries since they may differ in some aspects. Moreover, products of distinct but very similar genes or alternative splice products are included as separate entries. In some cases a more general term defining a S/MAR-binding activity may appear as one entry eventhough it might be composed of two or more subunits. The SMARbinder table will only contain those proteins of nuclear localization for which an interaction with a well defined S/MAR has been shown. Besides that the SMARbinder table will also include proteins that are proven components of the the salt-resitent (LIS-resistent) nuclear matrix. Gene entries, besides of giving the gene name in a long and a short (abbreviated) denomination, collect all links to individual S/MARs given in S/MARt DB and/or provide pointers to "S/MARbinders". The entries also contain links to transcription factor binding sites listed in TRANSFAC and give a link to the corresponding TRRD entry describing the regulatory features of the gene on different hierarchical levels.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a database dedicated to Receptor Tyrosine Kinase. The RTKdb is the web-based interface of the RTKdb which is a database containing all the protein sequences of RTK, organized into families. It allows one to select sets of homologous genes from different species (only common species for the moment) and to visualize multiple alignments and phylogenetic trees. Thus the RTKdb is particularly useful for comparative genomics, phylogeny and molecular evolution studies. It contains a total of 159 proteins.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of high throughput insertional mutagenesis screening projects of retroviral and transposon insertional mutagenesis in mouse tumors. Information in the RTCGD is obtained from sequence comparison by using public databases UCSC genome mm9 browser. Data based on previous genome assembly mm8 is also available at RTCGD mm8. MCGP has developed three web search tools including Easy Search to query proviral integration sites using mouse gene symbol of gene name; Model Search to obtain RIS information based on tumor models and/or tumor types; Interaction Search to find gene-to-gene interaction. It displays the list of genes which reside in the same tumor to your gene of interest.

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• SciCrunch
• 17 years ago - by Anonymous

Central repository for high quality frequently updated manual annotation of vertebrate finished genome sequence. Human, mouse and zebrafish are in the process of being completely annotated, whereas for other species the annotation is only of specific genomic regions of particular biological interest. The majority of the annotation is from the HAVANA group at the Welcome Trust Sanger Institute. Users can BLAST, search for specific text, export, and download data. Genomes and details of the projects for each species are available through the homepages for human mouse and zebrafish. The website is built upon code from the EnsEMBL (http://www.ensembl.org) project. Some Ensembl features are not available in Vega. From the users point of view perhaps the most significant of these is MartView. However due to their inclusion in Ensembl, Vega human and mouse data can be queried using Ensembl MartView. Vega contains annotation of the human MHC region in eight haplotypes, and the LRC region in three haplotypes. Vega also contains annotation on the Insulin Dependent Diabetes (IDD) regions on non-reference assemblies for mouse.

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• SciCrunch
• 16 years ago - by Anonymous

It is a database that details the interactions of extruded, unpaired RNA nucleotide bases. It presents and classifies the protein binding pockets that accommodate them, and also allows the recognition of similar protein binding patters involved in interactions with different RNA molecules. Given an unbound structure of a target protein, it allows the prediction of its RNA nucleotide binding sites. The goal of this database is to describe, classify, and predict the interactions between protein binding sites and single-stranded RNA bases. Specifically, RsiteDB describes the protein binding pockets that accommodate extruded nucleotides not involved in RNA base pairing. RsiteDB has two modes of operation. Analysis and classification of protein-RNA interactions: Given a protein-RNA complex RsiteDB analyzes its nucleotide and dinucleotide binding sites. It details the properties of the protein binding pockets that accommodate these extruded nucleotides and presents a list of proteins with similar binding pockets. These proteins may have a totally different overall sequences and structural folds. RsiteDB details and visualizes the features shared by all the binding sites classified to the same cluster. Prediction of RNA dinucleotide binding sites: Given a target, potentially unbound, protein structure we search its surface for regions similar to the created 3-D consensus binding patterns of RNA dinucleotides. The recognized regions are predicted to serve as binding sites. Using leave-one-out tests, the success rate of these predictions was estimated to be about 80%. It must be noted that currently we do not aim to predict whether a protein can bind RNA; rather, given an unbound RNA binding protein, our goal is to predict its binding sites and their modes of interaction. In addition, due to a low number of single nucleotide clusters, currently, we do not use them for the prediction.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a curated database that catalogs the numbers of genes that encode for 16S, 23S and 5S ribosomal RNAs in Bacteria and Archaea. Typically, a single copy of each of these genes is clustered into a rRNA operon, with as many as 15 rRNA operons present per genome. The genomic locus for any of the rRNA encoding genes is ?rrn? ? hence the name of this database. Because the number of genes encoding tRNAs is positively correlated with the number of rRNA-encoding genes (1), tRNA gene copy number is also cataloged in the rrnDB. Data are gathered both from sequenced genomes and from published articles that include estimates of the number of rRNA encoding genes.

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• SciCrunch
• 17 years ago - by Anonymous

It is a database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms. Users can search this database by gene name and organism. Each record includes sequences (genomic, cDNA, and amino acid sequences), intron/exon structures, genomic locations, and information about orthologs. In addition, users can view and compare the gene structures from different organisms and make multiple amino acid sequence alignments. RPG also provides information on small nucleolar RNAs (snoRNAs) that are encoded in the introns of RP genes.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. Database that offers information on molecules and interactions involving signaling pathways through literature-based curative explanation and laboratory results as well as basic information through links to other databases. Its major content consists of signaling entities and signaling interactions designed to describe various levels of signaling events. It is designed to convey chemical changes and logical information flow in detail through careful data modeling of complex signaling processes. ROSPath was developed for the purpose of aiding the research of ROS-mediated signaling pathways including growth factor-, stress- and cytokine-induced signaling that are main research interests of the Division of Molecular Life Sciences and Center for Cell Signaling Research in Ewha Womans University. ROSPath is designed to describe cellular signaling processes in molecular detail and to accumulate data and knowledge regarding signaling pathways with the organized database structure. It offers useful means to researchers by providing curative Information on the signaling pathways of interest and by providing means of managing data produced by high-throughput experiments such as proteomics and genomics tools. Furthermore, its goal is to provide effective and flexible tools for signaling pathway analysis and data mining by means of extensive data modeling and development of computer-aided tools.

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• SciCrunch
• 17 years ago - by Anonymous

It is a tool developed for RNR research that gives you the opportunity to retrieve RNR protein sequences from any organism that have been either experimentally characterised or predicted from genome sequence data. The RNR database contains a compilation of all published 3D structures of different RNR proteins as well as a compilation of all mutant proteins constructed including links to the relevant publication(s). RNRs by organism gives an overview of the entire database. Users can also search the database for occurrence of ribonucleotide reductases in taxonomic groups. The BLAST server of the RNR database allows sequences to be BLASTed against our database that contains RNR sequence, genomic, and species data.

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• SciCrunch
• 17 years ago - by Anonymous

Welcome to the computational genomics laboratory''s home page. Main research interests: computational biology, bioinformatics and systems biology applied to the study of the mechanisms underlying gene expression regulation. They also develop bioinformatic software aiming at helping the research community solve some problems.

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• SciCrunch
• 17 years ago - by Anonymous

It provides access to results from RNAi interference studies in C. elegans, including images, movies, phenotypes, and graphical maps. RNAiDB contains all published RNAi experiments in C. elegans that have been deposited in WormBase, including data from the literature and published large-scale RNAi studies. RNAi to gene mappings for all experiments have been re-analyzed using ePCR and/or a sliding n-mer window method to identify all genes in different genomic locations that may potentially be inhibited by each experiment. Gene maps showing canonical and putative alternate mappings are displayed graphically on RNAi Experiment and Gene/ORF card pages.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments (in species where more than one isolate has been fully sequenced) and contains translated genome sequences for all species. It has been created for two main purposes: to facilitate the comparative analysis of RNA viruses and to become a hub for other, more specialised virus Web sites.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 25, 2013. RISSC is a database of ribosomal 16S-23S spacer sequences intended mainly for molecular biology studies in typing, phylogeny and population genetics. Ribosomal spacers have proven to be extremely useful tools for typing and identifying closely related prokaryotes due to their high variability in size and/or sequence, much more so than the flanking 16S and 23S rRNA genes. These genes are commonly used to establish molecular relationships among microbes at a taxonomic level of species or higher (e.g genus, domain...). However their internal transcribed spacers (ITS) are much more useful to discriminate at the species or even strain level. Currently, many published papers are showing the growing importance of these regions of the ribosomal operon in these types of studies. A second, much shorter, ribosomal spacer can be found between rRNA genes 23S and 5S, also of phylogenetic interest. We intend to incorporate them into the database in the near future. By creating RISSC, our intention is to provide the scientific community with a comprehensive set of ribosomal spacer sequences, fully edited and characterized with a key feature as is the presence/absence of tRNA genes within them, ready to be used and compared with their own ITS sequences.

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• SciCrunch
• 17 years ago - by Anonymous