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http://www.megabionet.org/atpid/webfile/

Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.

Proper citation: Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) Copy   

•   Source: SciCrunch Registry

http://www.structuralgenomics.org/

The Structural Genomics Project aims at determination of the 3D structure of all proteins. It also aims to reduce the cost and time required to determine three-dimensional protein structures. It supports selection, registration, and tracking of protein families and representative targets. This aim can be achieved in four steps : -Organize known protein sequences into families. -Select family representatives as targets. -Solve the 3D structure of targets by X-ray crystallography or NMR spectroscopy. -Build models for other proteins by homology to solved 3D structures. PSI has established a high-throughput structure determination pipeline focused on eukaryotic proteins. NMR spectroscopy is an integral part of this pipeline, both as a method for structure determinations and as a means for screening proteins for stable structure. Because computational approaches have estimated that many eukaryotic proteins are highly disordered, about 1 year into the project, CESG began to use an algorithm. The project has been organized into two separate phases. The first phase was dedicated to demonstrating the feasibility of high-throughput structure determination, solving unique protein structures, and preparing for a subsequent production phase. The second phase, PSI-2, has focused on implementing the high-throughput structure determination methods developed in PSI-1, as well as homology modeling and addressing bottlenecks like modeling membrane proteins. The first phase of the Protein Structure Initiative (PSI-1) saw the establishment of nine pilot centers focusing on structural genomics studies of a range of organisms, including Arabidopsis thaliana, Caenorhabditis elegans and Mycobacterium tuberculosis. During this five-year period over 1,100 protein structures were determined, over 700 of which were classified as unique due to their < 30% sequence similarity with other known protein structures. The primary goal of PSI-1 was to develop methods to streamline the structure determination process, resulted in an array of technical advances. Several methods developed during PSI-1 enhanced expression of recombinant proteins in systems like Escherichia coli, Pichia pastoris and insect cell lines. New streamlined approaches to cell cloning, expression and protein purification were also introduced, in which robotics and software platforms were integrated into the protein production pipeline to minimize required manpower, increase speed, and lower costs. The goal of the second phase of the Protein Structure Initiative (PSI-2) is to use methods introduced in PSI-1 to determine a large number of proteins and continue development in streamlining the structural genomics pipeline. Currently, the third phase of the PSI is being developed and will be called PSI: Biology. The consortia will propose work on substantial biological problems that can benefit from the determination of many protein structures Sponsors: PSI is funded by the U.S. National Institute of General Medical Sciences (NIGMS),

Proper citation: Protein Structure Initiative (RRID:SCR_002161) Copy   

•   Source: SciCrunch Registry

http://www.candidagenome.org/

Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome.

Proper citation: Candida Genome Database (RRID:SCR_002036) Copy   

•   Source: SciCrunch Registry

http://biodev.extra.cea.fr/interoporc/

Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.

Proper citation: InteroPorc (RRID:SCR_002067) Copy   

•   Source: SciCrunch Registry

http://provean.jcvi.org/

A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

Proper citation: PROVEAN (RRID:SCR_002182) Copy   

•   Source: SciCrunch Registry

http://www.csardock.org

Experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets are generated in house while others are collected from the literature or deposited by academic labs, national centers, and the pharmaceutical industry. For the community to improve their approaches, they need exceptional datasets to train scoring functions and develop new docking algorithms. They aim to provide the highest quality data for a diverse collection of proteins and small molecule ligands. They need input from the community in developing target priorities. Ideal targets will have many high-quality crystal structures (apo and 10-20 bound to diverse ligands) and affinity data for 25 compounds that range in size, scaffold, and logP. It is best if the ligand set has several congeneric series that span a broad range of affinity, with low nanomolar to mid-micromolar being most desirable. They prefer Kd data over Ki data over IC50 data (no % activity data). They will determine solubility, pKa, logP/logD data for the ligands whenever possible. They have augmented some donated IC50 data by determining Kon/Koff and ITC data.

Proper citation: Community Structure-Activity Resource (RRID:SCR_002206) Copy   

•   Source: SciCrunch Registry

http://consurfdb.tau.ac.il/

Provides pre-calculated evolutionary conservation profiles for proteins of known structure in the PDB. Enables flexibility in setting the parameters of the calculation, and accepts optional uploads of atomic coordinates, multiple sequence alignments, and phylogenetic trees for use in the calculation of conservation profiles.

Proper citation: ConSurf Database (RRID:SCR_002320) Copy   

•   Source: SciCrunch Registry

http://www.glycosciences.de/

Portal of glycoinformatics resources including databases and bioinformatics tools for glycobiology and glycomics research. Databases include a bibliography, structure, nuclear magnetic resonance (NMR), mass spectroscopy (ms) and a PDB search.

Proper citation: glycosciences.de (RRID:SCR_002324) Copy   

•   Source: SciCrunch Registry

http://www.pharmabase.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2015. Open content cheminformatics database linking physiology with pharmacology, it targets the action and use of pharmacological compounds in modifying protein function, while revealing molecular relationships and linking out to related databases and sites. Pharmabase has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds in cellular research. It has several navigational routes, including a graphics browser (shows graphics of cell types and pathways) and membrane transport, which also illustrates the diversity of mechanisms that are covered. Users have access to detailed compound records with interactive features, and a form to send comments to the editor. Investigators are encouraged to alert the editors to mistakes, omissions or new compound information available from their reading and research.

Proper citation: Pharmabase - an open content cheminformatics resource linking physiology with pharmacology (RRID:SCR_002462) Copy   

•   Source: SciCrunch Registry

http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

•   Source: SciCrunch Registry

http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html

A database of protein subcellular localization containing proteins from primary protein database SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross references to taxonomies and Gene Ontology database. Annotations were taken from primary protein databases, model organism genome projects and literature texts, and then were analyzed to dig out the subcellular localization features of the proteins. The proteins are also classified into different categories. Based on sequence alignment, nonredundant subsets of the database have been built, which may provide useful information for subcellular localization prediction. The database now contains >60 000 protein sequences including 30 000 protein sequences in the nonredundant data sets. Online download, SOAP server, Blast tools and prediction services are also available.

Proper citation: DBSubLoc - Database of protein Subcellular Localization (RRID:SCR_002339) Copy   

•   Source: SciCrunch Registry

http://www.humgen.rwth-aachen.de/

Catalog of all changes detected in PKHD1 (Polycystic Kidney and Hepatic Disease 1) in a locus specific database. Investigators are invited to submit their novel data to this database. These data should be meaningful for clinical practice as well as of relevance for the reader interested in molecular aspects of polycystic kidney disease (PKD). There are also some links and information for ARPKD patients and their parents. Autosomal recessive polycystic kidney disease (ARPKD/PKHD1) is an important cause of renal-related and liver-related morbidity and mortality in childhood. This study reports mutation screening in 90 ARPKD patients and identifies mutations in 110 alleles making up a detection rate of 61%. Thirty-four of the detected mutations have not been reported previously. Two underlying mutations in 40 patients and one mutation in 30 cases are disclosed, and no mutation was detected on the remaining chromosomes. Mutations were found to be scattered throughout the gene without evidence of clustering at specific sites. PKHD1 mutation analysis is a powerful tool to establish the molecular cause of ARPKD in a given family. Direct identification of mutations allows an unequivocal diagnosis and accurate genetic counseling even in families displaying diagnostic challenges.

Proper citation: Autosomal Recessive Polycystic Kidney Disease Mutation Database (RRID:SCR_002290) Copy   

•   Source: SciCrunch Registry

http://reflect.embl.de/

Web service that tags gene, protein, and small molecule names in any web page. Clicking on a tagged term opens a small popup showing summary information, and allows the user to quickly link to more detailed information. For each protein or gene, Reflect provides domain structure, sub-cellular localization, 3D structure, and interaction partners. For small molecules, it provides the chemical structure and interaction partners. Reflect can be installed as a plugin to Firefox or Internet Explorer, or can be used by entering a URL in the field provided. It can also be accessed programmatically via a REST or SOAP API, and a Reflect button can easily be added to any web page using Javascript or using a CGI proxy. Reflect was first-prize winner out of over 70 submissions in the Elsevier Grand Challenge, an international competition for systems that improve the way scientific information is communicated and used. Reflect can be edited and improved by the community.

Proper citation: Reflect (RRID:SCR_002714) Copy   

•   Source: SciCrunch Registry

http://www.Ablynx.com

A biopharmaceutical company engaged in the discovery and development of Nanobodies, a novel class of antibody-derived therapeutic proteins based on single-domain antibody fragments, for a range of serious life-threatening human diseases including inflammation, hematology, oncology and pulmonary disease.

Proper citation: Ablynx (RRID:SCR_002940) Copy   

•   Source: SciCrunch Registry

http://proteininformationresource.org/

Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO.

Proper citation: Protein Information Resource (RRID:SCR_002837) Copy   

•   Source: SciCrunch Registry

http://www.gramene.org

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Proper citation: Gramene (RRID:SCR_002829) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/msa/clustalw2/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF.

Proper citation: Clustal W2 (RRID:SCR_002909) Copy   

•   Source: SciCrunch Registry

http://www.cephalopod.org/DBMR.cfm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The center serves the biomedical research community's increased needs for alternative invertebrate models by maintaining a consistent year-round supply of live cephalopod mollusks. These animals are suitable for a wide range of physiological and molecular biological investigations. Investigations are being conducted in the area of life history related to improved animal husbandry. Further studies focus on improving culture system design through development of computer automation and innovative water filtration technology. Current biomedical research on cephalopods includes neurophysiology of the giant axon; anatomy and neurophysiology of the equilibrium receptor organ as a comparative model of the vestibular system of invertebrates; chemoreception, basic nutrition, and protein metabolism; cellular receptor function; and brain, behavior, and learning. Services Provided: The center has built a computer-automated, environmentally controlled, recirculating seawater laboratory for the purpose of culturing cephalopods. The tank systems can be used to conduct a variety of experiments never before possible with cephalopods. Visiting researchers have access to dedicated facilities, including wet and dry laboratory space, office space, computer support and accommodations, as well as priority access to all available live animal resources. Off-site investigators can have live animals, dissected animal tissues/body fluids from all life stages, and a variety of molecular reagents (gene libraries and clones) delivered year-round. Staff expertise and an extensive literature library are available. All life stages of the squid (Sepioteuthis lessoniana) and the common cuttlefish (Sepia officinalis) are available year-round from laboratory culture populations. The sepiolid squid (Euprymna scolopes) can also be cultured on request. The squid Lolliguncula brevis is available year-round from local waters; the squids Loligo opalescens, L. pealeii, and L. plei can be obtained seasonally on request. The chambered nautilus, Nautilus pompilius, and Octopus bimaculoides are available on request. Animal costs vary by species and size. Any tissue or body fluid from these animals can also be provided. Fees for special services are negotiated on a case-by-case basis.

Proper citation: National Resource Center for Cephalopods (RRID:SCR_002864) Copy   

•   Source: SciCrunch Registry

http://gemdock.life.nctu.edu.tw/3D-Interologs

Database of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins.

Proper citation: 3D-Interologs (RRID:SCR_003101) Copy   

•   Source: SciCrunch Registry

http://cal.tongji.edu.cn/PlantLoc/index.jsp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif.

Proper citation: PlantLoc (RRID:SCR_003138) Copy   

•   Source: SciCrunch Registry