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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://pir.georgetown.edu/pro/

An ontological representation of protein-related entities, explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. PRO encompasses three sub-ontologies: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).

Proper citation: PRO (RRID:SCR_002902) 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://elm.eu.org

Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.

Proper citation: Eukaryotic Linear Motif (RRID:SCR_003085) Copy   

•   Source: SciCrunch Registry

http://www.diabetesgenome.org

Produce resources to unravel the interface between insulin action, insulin resistance and the genetics of type 2 diabetes including an annotated public database, standardized protocols for gene expression and proteomic analysis, and ultimately diabetes-specific and insulin action-specific DNA chips for investigators in the field. The project aims to identify the sets of the genes involved in insulin action and the predisposition to type 2 diabetes, as well as the secondary changes in gene expression that occur in response to the metabolic abnormalities present in diabetes. There are five major and one pilot project involving human and rodent tissues that are designed to: * Create a database of the genes expressed in insulin-responsive tissues, as well as accessible tissues, that are regulated by insulin, insulin resistance and diabetes. * Assess levels and patterns of gene expression in each tissue before and after insulin stimulation in normal and genetically-modified rodents; normal, insulin resistant and diabetic humans, and in cultured and freshly isolated cell models. * Correlate the level and patterns of expression at the mRNA and/or protein level with the genetic and metabolic phenotype of the animal or cell. * Generate genomic sequence from a panel of humans with type 2 diabetes focusing on the genes most highly regulated by insulin and diabetes to determine the range of sequence and expression variation in these genes and the proteins they encode, which might affect the risk of diabetes or insulin resistance. The DGAP project will define: * the normal anatomy of gene expression, i.e. basal levels of expression and response to insulin. * the morbid anatomy of gene expression, i.e., the impact of diabetes on expression patterns and the insulin response. * the extent to which genetic variability might contribute to the alterations in expression or to diabetes itself.

Proper citation: DGAP (RRID:SCR_003036) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/dalilite/indexhtml

Tool that computes optimal and suboptimal structural alignments between two protein structures. It will compare all chains in the first structure against all chains in the second (unless specific chain IDs are given). The resulting superimposed coordinate files can be downloaded or viewed interactively in Jmol. The Dali method optimizes a weighted sum of similarities of intramolecular distances. Suboptimal alignments do not overlap the optimal alignment or each other. Suboptimal alignments detected by the program are reported if the Z-score is above 2; they may be of interest if there are internal repeats in either structure. SOAP Web services are also available.

Proper citation: DaliLite Pairwise comparison of protein structures (RRID:SCR_003047) Copy   

•   Source: SciCrunch Registry

http://www.abazyme.com/

Commercial antibody supplier that provides reagents such as immunoassay kits, antibodies, and proteins as well as custom services such as antigen preparation, sequencing and engineering.

Proper citation: Abazyme (RRID:SCR_001139) Copy   

•   Source: SciCrunch Registry

https://atlasantibodies.com/

An antibody supply company that provides reagents targeting all human proteins. Atlas Antibodies develops reagents and antibodies for mass-spectrometry-based quantitative proteomics as well. Their production and development is based on the Human Protein Atlas (HPA) project, which released a complete tissue-based map of human protein expression using antibodies.

Proper citation: Atlas Antibodies (RRID:SCR_001137) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/services/NetNGlyc-1.0/

Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms.

Proper citation: NetNGlyc (RRID:SCR_001570) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/services/YinOYang-1.2/

Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms.

Proper citation: YinOYang (RRID:SCR_001605) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/jdispatcher/msa/clustalo?stype=protein

Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.

Proper citation: Clustal Omega (RRID:SCR_001591) Copy   

•   Source: SciCrunch Registry

http://iclab.life.nctu.edu.tw/iclab_webtools/sodock/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems.

Proper citation: SODOCK (RRID:SCR_000193) Copy   

•   Source: SciCrunch Registry

http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp

A complete drug designing software suite with an accessible web-server for targeted directed lead molecule discovery.

Proper citation: Sanjeevini (RRID:SCR_000191) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/as-peak/

A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.

Proper citation: AS-Peak (RRID:SCR_000380) Copy   

•   Source: SciCrunch Registry

http://thomsonreuters.com/metadrug/

A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization

Proper citation: MetaDrug (RRID:SCR_000461) Copy   

•   Source: SciCrunch Registry

http://dbserv2.informatik.uni-leipzig.de:8080/onex/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released

Proper citation: OnEx - Ontology Evolution Explorer (RRID:SCR_000602) Copy   

•   Source: SciCrunch Registry

http://megasoftware.net/

Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.

Proper citation: MEGA (RRID:SCR_000667) Copy   

•   Source: SciCrunch Registry