Tools   Select Another Resource Report Type

http://saxs.ifsc.usp.br/

Software tool as online calculator of molecular weight of proteins in dilute solution from experimental SAXS data measured on relative scale. Software package for easy processing of small angle X ray scattering data from mono disperse systems in diluted solution.

Proper citation: SAXS Molecular Weight (RRID:SCR_018137) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/AutoEVM

Software tool as Autorun Evidence Modeler. Requires EVidenceModeler (aka EVM) software which combines ab into gene predictions and protein and transcript alignments into weighted consensus gene structures.

Proper citation: AutoEVM (RRID:SCR_017556) Copy   

•   Source: SciCrunch Registry

http://www.molecularconnections.com/home/en/home/products/netPro

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Comprehensive database of Protein-Protein and Protein-Small molecules interaction, consisting of more than 320,000 interactions captured from more than 1500 abstracts, approximately 1600 published journals and more than 60,000 references. The strength of NetPro lies in the complete manual curation of literature. It covers several entities other than proteins as interacting partners, like RNA, DNA, processes, etc. with well defined, exhaustive interaction terms. NetPro has received several accolades for the quality and quantity of data it contains. It has become an important resource for target identification, validation and pathway research and has subscribers from all over the globe including 3 of the top 5 pharmas.

Proper citation: Molecular Connections NetPro (RRID:SCR_000395) Copy   

•   Source: SciCrunch Registry

http://psychiatry.igm.jhmi.edu/SynaptomeDB/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Ontology-based knowledgebase for synaptic genes. These genes encode components of the synapse including neurotransmitters and their receptors, adhesion / cytoskeletal proteins, scaffold proteins, transporters, and others. It integrates various and complex data sources for synaptic genes and proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SynaptomeDB (RRID:SCR_000157) Copy   

•   Source: SciCrunch Registry

http://www.bindingdb.org

Web accessible database of data extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in Protein Data Bank . Website supports query types including searches by chemical structure, substructure and similarity, protein sequence, ligand and protein names, affinity ranges and molecular weight . Data sets generated by BindingDB queries can be downloaded in form of annotated SDfiles for further analysis, or used as basis for virtual screening of compound database uploaded by user. Data are linked to structural data in PDB via PDB IDs and chemical and sequence searches, and to literature in PubMed via PubMed IDs .

Proper citation: BindingDB (RRID:SCR_000390) Copy   

•   Source: SciCrunch Registry

http://text0.mib.man.ac.uk/software/mldic/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. System that retrieves relevant UniProt IDs from BioThesaurus entries using a soft string matching algorithm.

Proper citation: Smart Dictionary Lookup (RRID:SCR_000568) Copy   

•   Source: SciCrunch Registry

http://www.dpidb.genebee.msu.ru/

The database NPIDB (Nucleic acid Protein Interaction DataBase) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from Protein Data Bank (PDB) (1932 complexes in the end of 2007). It is equipped with a web-interface and a set of tools for extracting biologically meaningful characteristics of complexes. They are committed to satisfy all potential database users in order to: 1. Provide an essential information on structural features of DNA-protein and RNA-protein interaction for the users who need to get acquainted with the problem. 2. Give an effective access to the reasonably structured information about all DNA-protein and RNA-protein complexes containing in PDB. 3. Allow all visitors a quick access to our own research.

Proper citation: DNA-Protein Interaction Database (RRID:SCR_000754) Copy   

•   Source: SciCrunch Registry

http://www.ampdb.bcs.uwa.edu.au/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. The Arabidopsis Mitochondrial Protein Database is an Internet-accessible relational database containing information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana. This database, and the proteomic data contained in it for Arabidopsis mitochondria, have been accepted for publication in The Plant Cell.

Proper citation: AMPDB: Arabidopsis Mitochondrial Protein Database (RRID:SCR_000758) Copy   

•   Source: SciCrunch Registry

http://www.biorag.org/index.php

Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona.

Proper citation: Bio Resource for Array Genes Database (RRID:SCR_000748) Copy   

•   Source: SciCrunch Registry

http://mitominer.mrc-mbu.cam.ac.uk/

A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java.

Proper citation: MitoMiner (RRID:SCR_001368) Copy   

•   Source: SciCrunch Registry

http://webclu.bio.wzw.tum.de/dima/

DIMA, the Domain Interaction Map, aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains. The scope of the resource comprises both experimental data and computational predictions. Several methods and datasets have been integrated, already and inclusion of others is under way.

Proper citation: Domain Interaction MAp (RRID:SCR_000731) Copy   

•   Source: SciCrunch Registry

http://www.ispybio.com/

Search engine for Life scientists that ranks reagents by the amount of data available, such as publications, reviews, characterization images and tested applications. It displays reagents such as antibodies, proteins, ELISA kits and biomolecules. Its proprietary search algorithm is unique and rapidly analyzes the end-user's search query against its large database, while powerful filters allow the user to enhance search results. As iSpyBio syncs with supplier and other public databases, it is always up-to-date - allowing iSpyBio to exclude out of stock items, whilst also showing the most recent testing results and peer-reviewed publications.

Proper citation: iSpyBio.com (RRID:SCR_000465) Copy   

•   Source: SciCrunch Registry

http://crbs.ucsd.edu/

CRBS is a UCSD organized research unit (ORU) that exists to provide human resources, high technology equipment, and administrative services to researchers engaged in fundamental research on cell structure and function relationships in central nervous system processes, cardiovascular networking, and muscular contraction through multiple scales and modalities. CRBS scientists investigate these processes through invention, refinement, and deployment of sophisticated technologies, especially: - High-powered electron microscopes that reveal three-dimensional cell structures - State-of-the-art X-ray crystallography and magnetic resonance analysis that provide detail on protein structures at high-resolution - Laser-scanning and confocal light microscopes that reveal molecules tagged with fluorescent markers as they traffic within cells and pass transfer signals within and between cells - High performance computing and grid-based integration of distributed data CRBS facilitates an interdisciplinary infrastructure in which people from biology, medicine, chemistry, and physics can work with those from computer science and information technologies in collaborative research. Researchers share interests in the study of complex biological systems at many scales, from the structures of enzymes, proteins, and the body's chemical communications network at atomic and molecular levels, to an organism's physiology, strength, and support at cellular and tissue levels. The CRBS infrastructure integrates resources for high-performance computing, visualization, and database technologies, and the grid-integration of large amounts of archival storage data. The California Institute for Telecommunications and Information Technology (Cal-IT2) and the San Diego Supercomputer Center (SDSC) are collaborators in simulating the activity of biological systems, analyzing the results, and organizing the growing storehouse of biological information. CRBS is an entity evolving as research evolves. It forges interactions with biotechnology and biocomputing companies for technology transfer. Interaction, collaboration, and multiscale research produce new perspectives, reveal fruitful research topics, lead to the development of new technologies and drugs, and train a new generation of researchers in biological systems. Sponsors: CRBS is supported by the University of California at San Diego.

Proper citation: Center for Research in Biological Systems (RRID:SCR_002666) Copy   

•   Source: SciCrunch Registry

http://www.cs.ualberta.ca/~bioinfo/PA/GOSUB/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 30, 2015. Refer to Proteome Analyst 3.0. Subcellular Localization and GO General Molecular Function predictions for many model organism proteomes using Protein Analyst, with a very high coverage rate. When users blast their proteins against the database of results, they will not only be shown blast homologs from the model organisms, but also the Subcellular Localization and GO General Molecular Function predictions as well.

Proper citation: Proteome Analyst PA-GOSUB (RRID:SCR_008234) Copy   

•   Source: SciCrunch Registry

http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/

Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible

Proper citation: STRAP (RRID:SCR_005675) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/blast2/index.html

It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterized genes.

Proper citation: Washington University Basic Local Alignment Search Tool (RRID:SCR_008285) Copy   

•   Source: SciCrunch Registry

http://www.uwstructuralgenomics.org/

It is a specialized research center supported by the Protein Structure Initiative (PSI) of the National Institute of General Medical Sciences (NIGMS), one of the National Institutes of Health (NIH). PSI is a federal, university, and industry effort aimed at dramatically reducing the costs and lessening the time it takes to determine a three-dimensional protein structure. The long-range goal of PSI is to solve 10,000 protein structures in 10 years and to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences. CESG is located within the Department of Biochemistry at the University of Wisconsin-Madison (Madison, WI) and the Department of Biochemistry at the Medical College of Wisconsin (Milwaukee, WI). CESG develops new methods and technologies to address unique eukaryotic bottlenecks and disseminates its methodologies and experimental results to the scientific community worldwide through: :- Cell-Free Protein Production Workshops :- Plasmids at PSI Materials Repository :- Posters Presented at Scientific Meetings :- Publications in PubMed / PubMed Central :- Sesame (LIMS) Available for Researchers :- Solved Structures in the Protein Data Bank :- Technology Dissemination Reports They have welcomed requests by researchers to solve eukaryotic protein structures, particularly medically relevant proteins, through our Online Structure Request System for Researchers. They have solved many community-nominated targets and deposited information about these targets in public databases and published on our investigations and findings. Sponsors: CESG is supported by NIH / NIGMS Protein Structure Initiative grant numbers U54 GM074901 and P50 GM064598.

Proper citation: CESG (RRID:SCR_008451) Copy   

•   Source: SciCrunch Registry

http://expasy.org/

Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. It contains resources from many different SIB groups as well as external institutions.

Proper citation: ExPASy Bioinformatics Resource Portal (RRID:SCR_012880) Copy   

•   Source: SciCrunch Registry

http://lab.rockefeller.edu/chait/

Biomedical technology research center that develops cutting-edge mass spectrometric tools for analyzing peptides and proteins. It makes its software tools developed for data analysis freely available.

Proper citation: National Resource for the Mass Spectrometric Analysis of Biological Macromolecules (RRID:SCR_009007) Copy   

•   Source: SciCrunch Registry

http://hollow.sourceforge.net/

HOLLOW facilitates the production of surface images of proteins. HOLLOW is a portable command-line utility written in Python 2.4-2.7; it does not have any other dependencies (although running under the PyPy JIT interpreter, it runs much faster). The input is a PDB file. The output is a PDB file of dummy water atoms that forms a cast of the voids and channels of a protein. HOLLOW generates a surface from a cast of the protein surface. HOLLOW fills the interior spaces of a protein structure with dummy atoms defined on an overlapping grid. The surface generated by these dummy atoms can be shown to reproduce the surface of the protein at the ideal limit. The use of the surface of the dummy atoms allows us to focus on a specific piece of the interior surface. Simply by deleting dummy atoms, the interior surface can be trimmed to produce a custom portion of the interior space. For advanced coloring of the surface, the B-factor of the dummy atoms can be calculated as the average of the B-factor of the protein atoms surrounding the dummy atoms. This allows various colorings of the surface to be conveyed through the B-factor field of the PDB files. The volume filling representation facilitated by HOLLOW is meant to complement other programs that identify voids, pockets and channels, such as SPHGEN and CASTp, which identify binding sites but cannot produce output that can be rendered in standard molecular graphics software. HOLLOW can be used to help render these binding pockets.

Proper citation: HOLLOW (RRID:SCR_005729) Copy   

•   Source: SciCrunch Registry