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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
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
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
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
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
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
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
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
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
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
The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin.
Proper citation: EMBL - Bork Group (RRID:SCR_000810) Copy
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
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
A protein family specific platform that works closely with the GPCR community to determine the high resolution structure and function of GPCRs. Structures are available in the glutamate, secretin, frizzled/TAS2, adhesion, and rhodopsin branches of the protein phylogenetic tree. Users can access a list of protein structure targets and completed protein structures.
Proper citation: GPCR Network (RRID:SCR_014286) Copy
http://www.matrixscience.com/server.html
A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters.
Proper citation: Mascot (RRID:SCR_014322) Copy
A a configurable software package for peptide and protein mass spectrometry analyses. It includes the SEQUEST search algorithm to identify separate proteins in complex mixtures, interactive navigation tools to filter and sort protein summaries, customized spectral plots, and chromatograms using the PEPMATCH and PEPMAP tools. This software also has batch processing capabilities to improve throughput by queuing up several files, and custom-build proprietary databases, index databases, and retrieve databases through a public server.
Proper citation: BioWorks (RRID:SCR_014594) Copy
Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: FATCAT (RRID:SCR_014631) Copy
Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers.
Proper citation: GROMACS (RRID:SCR_014565) Copy
http://www.molsoft.com/icm_browser.html
Molecular graphics environment which provides biologists and chemists with representations of proteins, DNA, RNA, and multiple sequence alignments. Users can build, annotate, and edit interactive views and slides of molecules. Users can also superimpose protein structures, search PDB, measure distanaces and angles, and view and make high resolution images of alignments.
Proper citation: ICM Browser (RRID:SCR_014878) Copy
http://prosightlite.northwestern.edu/
Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.
Proper citation: ProSight Lite (RRID:SCR_016908) Copy
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