Curator Dashboard

Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal.

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• SciCrunch
• 17 years ago - by Anonymous

It is a web-server that can be used to explore protein interfaces and predict protein-protein interactions. It is a website for protein interface analysis and prediction of putative protein-protein interactions. It is composed of a database holding protein interface structures derived from the Protein Data Bank (PDB). The server also includes summary information about related proteins and an interactive protein interface viewer. A list of putative protein-protein interactions obtained by running our prediction algorithm can also be accessed. These results are applied to a set of protein structures obtained from the PDB at the time of algorithm execution. Users can browse through the non-redundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of similar structures to these interfaces or see the results of interaction predictions for a particular protein. Another service provided is interactive prediction. This is done by running the algorithm for user input structures.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. iPfam is a resource that describes physical interactions between those Pfam domains that have a representative structure in the Protein DataBank (PDB). When two or more domains occur within a single structure, the domains are analysed to see if they form an interaction. If the domains are close enough to form an interaction, the bonds that play a role in that interaction are determined. The goal has been to re-calculate iPfam interaction data for each new Pfam release, so that, as Pfam changes, the information within iPfam remains up to date.

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• SciCrunch
• 17 years ago - by Anonymous

Commercial supplier of antibodies, reagents, and dyes for research.

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• SciCrunch
• 14 years ago - by Anonymous

Database of Drosophila transcription factor DNA binding specificity using the bacterial one-hybrid method, DNase I or SELEX methods. The database provides community access to recognition motifs and position weight matrices for transcription factors (TFs), including many unpublished motifs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within the database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome. This database and its associated tools provide computational and experimental biologists with resources to predict interactions between Drosophila TFs and target cis-regulatory sequences.

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• SciCrunch
• 13 years ago - by Anonymous

Database of non-redundant sets of protein - small-molecule complexes that are especially suitable for structure-based drug design and protein - small-molecule interaction research. PSMB supports: * Support frequent updates - The number of new structures in the PDB is growing rapidly. In order to utilize these structures, frequent updates are required. In contrast to manual procedures which require significant time and effort per update, generation of the PSMDB database is fully automatic thereby facilitating frequent database updates. * Consider both protein and ligand structural redundancy - In the database, two complexes are considered redundant if they share a similar protein and ligand (the protein - small-molecule non-redundant set). This allows the database to contain structural information for the same protein bound to several different ligands (and vice-versa). Additionally, for completeness, the database contains a set of non-redundant complexes when only protein structural redundancy is considered (our protein non-redundant set). The following images demonstrate the structural redundancy of the protein complexes in the PDB compared to the PSMDB. * Efficient handling of covalent bonds -Many protein complexes contain covalently bound ligands. Typically, protein-ligand databases discard these complexes; however, the PSMDB simply removes the covalently bound ligand from the complex, retaining any non-covalently bound ligands. This increases the number of usable complexes in the database. * Separate complexes into protein and ligand files -The PSMDB contains individual structure files for both the protein and all non-covalently bound ligands. The unbound proteins are in PDB format while the individual ligands are in SDF format (in their native coordinate frame).

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• SciCrunch
• 17 years ago - by Anonymous

It helps molecular cell biologists manage and test their increasingly complex mechanistic hypotheses. ProcessDB does this with a bio-savvy graphical user interface that helps users formulate, visualize, compare, modify, manage and test their own mechanistic theories of cellular function. All models in ProcessDB can be automatically combined with user-specified experimental protocols and exported to the Berkeley Madonna solver for testing against experimental data. ProcessDB allows investigators to know with precision what their theories predict, and speeds discovery of mechanisms that account for all of the available data. ProcessDB, which is accessable from any Internet-connected computer, offers a highly secure and professionally maintained tool that supports mechanistic knowledge management for research laboratories working on complex biological or biomedical problems.

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• SciCrunch
• 17 years ago - by Anonymous

Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A comprehensive human kinase interactome and phospho-protein database. PhosphoPOINT also annotates any amino acids near the phosphorylation sites where a cSNP may cause a phosphorylation site to be lost, and at the same time identifies how such alteration of the phosphorylation site may lead to human disease. PhosphoPOINT integrates 4,195 phospho-proteins, 518 serine/threonine/tyrosine kinases, and their corresponding PPI datasets with the goal of delineating the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. PhosphoPOINT has integrated human protein kinases, phospho-proteins, and PPI datasets with the goal to delineate four kinds of links among kinases. These include their interacting proteins, substrates, and substrates as well as interacting phospho-proteins. Some of these interacting proteins for kinases are phospho-proteins, which might have the potential to serve as substrates for the interacting kinases.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web application used to exploration of protein pathways. It provides analysis and navigation within networks, overviews of biological connections between proteins, access to relevant literature and annotations, and comparisons of interaction and functional domains.

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• SciCrunch
• 17 years ago - by Anonymous

A database of new exon boundaries induced by pathogenic mutations in human disease genes.

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• SciCrunch
• 13 years ago - by Anonymous

A free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser. This list can be restricted by the user to either only a specific region in the genome (by specifying the chromosome, the strand and the start and end position), to a whole chromosome or to a group of genes. Furthermore, exons can be filtered according to their splicing type (constitutive exons, cassette exons and exons with one or more alternative 3' and/or 5' splice sites). In order to extract a customized set of exons, the user-specific definitions of exon types can be fixed. The user needs to specify in what fraction of ESTs an exon is allowed to be alternatively spliced in order to still be called constitutive. Furthermore, the user can restrict the set of requested cassette exons by a certain upper inclusion level, which, for instance, is useful when only looking for low-inclusion exons.

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• SciCrunch
• 13 years ago - by Anonymous

Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.

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• SciCrunch
• 14 years ago - by Anonymous

Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013)

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• SciCrunch
• 17 years ago - by Anonymous

A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A comprehensive collection of manually curated information from literature as well as public domain databases on signaling and metabolic pathways. PathArt includes a dynamic pathway articulator component, which builds molecular interaction networks from curated databases. PathArt provides a tool for analysis, biological interpretation and visualization of microarray data results in these curated pathways. In addition, PathArt provides a collection of high priority disease and physiology pathways with emphasis on pathway responsive genes and knockouts. The coverage is for pathways of Human, Rat and Mouse for cell specific, tissue specific and organism specific data. The present version of PathArt covers the following: -Includes 3527 regulatory and signaling pathways across diseases and physiologies. -Provides information on 39 high priority diseases, and pathway and disease responsive genes. -Provides pathway information on 23 diverse physiologies. -Covers information on ~8783 Knockouts and ~18000 mutation data points. -Coverage of pathways for Human, Mouse and Rat for cell specificity, tissue specificity and organism specific data.

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• SciCrunch
• 17 years ago - by Anonymous

The human pathway database which contains different biological entities and reactions and software tools for analysis. PATIKA Database integrates data from several sources, including Entrez Gene, UniProt, PubChem, GO, IntAct, HPRD, and Reactome. Users can query and access this data using the PATIKAweb query interface. Users can also save their results in XML or export to common picture formats. The BioPAX and SBML exporters can be used as part of this Web service.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IS SERVICE. Documented on July,29,2022. Surface-based atlases of human, macaque, rat and mouse cerebral and cerebellar cortices derived from structural MRI volumes developed in the Van Essen laboratory can be downloaded by direct links on the SumsDB database and can be viewed using freely available Caret (offline) and WebCaret (online) software. The human and macaque atlases include a large and growing compendium of experimental data pertaining to the structural and functional organization of primate cerebral cortex.

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• SciCrunch
• 17 years ago - by Anonymous

Database for conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. The database offers information on atomic motifs, motif groups and patterns. In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, a base set of probabilistic ab initio discovery tools is used, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes. In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species.

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• SciCrunch
• 17 years ago - by Anonymous

A database of proteins and RNAs that have been identified in various purified splicing complexes. Various names, orthologs and gene identifiers of spliceosome proteins have been cataloged to navigate the complex nomenclature of spliceosome proteins. Links to gene and protein records are also provided for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, tools were created to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes.

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• SciCrunch
• 13 years ago - by Anonymous