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http://zhanglab.ccmb.med.umich.edu/I-TASSER/

Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation.

Proper citation: I-TASSER (RRID:SCR_014627) Copy   

•   Source: SciCrunch Registry

http://www.ccdc.cam.ac.uk/free_services/relibase_free

Web-based system for searching and analysing protein-ligand structures in the Protein Data Bank (PDB). The database provides an easily accessible web-browser interface and clear 3D structure visualisation that allows for 3D protein-ligand interaction searches, automatic superimposition and detailed analysis of related binding sites to identify protein flexibility, ligand overlap, and conserved water positions.

Proper citation: Relibase (RRID:SCR_014888) Copy   

•   Source: SciCrunch Registry

https://www.encodeproject.org/

Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present.

Proper citation: Encode (RRID:SCR_015482) Copy   

•   Source: SciCrunch Registry

https://omictools.com/rnacompete-tool

Method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. RNAcompete identifies expected and previously unknown RNA binding preferences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RNAcompete (RRID:SCR_015900) Copy   

•   Source: SciCrunch Registry

http://orphelia.gobics.de/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment.

Proper citation: Orphelia (RRID:SCR_000119) Copy   

•   Source: SciCrunch Registry

http://www.gobics.de/fabian/treephyler.php

A software tool for fast taxonomic profiling of metagenomes.

Proper citation: Treephyler (RRID:SCR_000109) Copy   

•   Source: SciCrunch Registry

http://www.conplot.org/

Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein.

Proper citation: ConPlot (RRID:SCR_019216) Copy   

•   Source: SciCrunch Registry

http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH

Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt.

Proper citation: Embassy-domsearch (RRID:SCR_016086) Copy   

•   Source: SciCrunch Registry

https://www.nist.gov/srd/nist-standard-reference-database-1a-v14

A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals.

Proper citation: Mass Spectral Library (RRID:SCR_014668) Copy   

•   Source: SciCrunch Registry

https://prokoplab.com/vistedd/

Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein.

Proper citation: Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) Copy   

•   Source: SciCrunch Registry

http://epsd.biocuckoo.org/

Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies.

Proper citation: EPSD Eukaryotic Phosphorylation Site Database (RRID:SCR_016514) Copy   

•   Source: SciCrunch Registry

http://www.mrmatlas.org/

Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome.

Proper citation: SRMAtlas (RRID:SCR_016996) Copy   

•   Source: SciCrunch Registry

https://www.alzforum.org/alzpedia

Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge.

Proper citation: ALZPEDIA (RRID:SCR_017548) Copy   

•   Source: SciCrunch Registry

http://specimencentral.com/

World's open biospecimen research database where biobanks and biomedical researchers meet to exchange human biospecimen needs and supply: whole blood, serum, plasma, solid tissue samples and more. The connection is accelerated so researchers save valuable time and money and tissue banks utilize inventory. The pace of specimen procurement remains unacceptably slow to the biomedical research community. Specimen Central is the foremost global resource to aid biomedical researchers in expediting their search for high quality human biospecimens, tissues, samples and specimens. They facilitate your search for blood, whole blood, buccal swab, DNA, RNA, protein, cell lines, plasma, serum, RBC, white cells, buffy coat, fluid, marrow, urine, stem cells, and solid tissue such as tumor, tumor and biopsy materials spanning all manner of common and rare pathologies and indications including Alzheimer's, basal cell carcinoma, bladder cancer, bone cancer, brain cancer, breast cancer, cerebrospinal fluid, amniotic fluid, colorectal cancer, colon cancer, hodgkins and non-hodgkins lymphoma, kidney/renal cancer, leukemia, liver cancer, lung cancer, melanoma, multiple sclerosis, myeloma neuroblastoma, neurodegenerative diseases, ovarian cancer, pancreatic cancer, prostate cancer, urinary cancer. This includes adult and pediatric indications. Specimen Central users specify a number of variables in their Specimen Requests, including preparation, preservation and handling requirements such as cryo-preserved, FFPE (Formalin-fixed paraffin-embedded), formalin, frozen, refrigerated, OCT, snap frozen, paraffin block, fresh, prospective, autopsy or cadaveric, etc. Many users require clinically annotated date associated with their specimens, as well as documentation of IRB or ethics committee approval and informed consents. For Researchers Most specimen databases require researchers to waste time and effort entering lengthy registrations and search queries that yield poor results, if anything. Specimen Central solves this problem by having tissue banks search for you. From years to months, months to weeks, and weeks to days, Specimen Central seeks to reduce delays and costs in the research & development life cycle by expediting connections between demand and supply. For Biobanks The capital costs of maintaining a biobank infrastructure are substantial and growing. Biobanks use Specimen Central as a marketing tool to augment their business development efforts. By routinely checking Specimen Central's Specimen Requests, biobanks can uncover market demand for their inventories and develop new connections and revenue streams to defray costs. Specimen Central supplements - not displaces - the efforts of your sales representatives, agents, brokers and commercial partners.

Proper citation: SpecimenCentral.com (RRID:SCR_003536) Copy   

•   Source: SciCrunch Registry

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

The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics. These are subdivided into categories in the left menu for convenience. EBI has developed a large number of very useful bioinformatics tools. A few examples include: - Similarity & Homology - the BLAST or FASTA programs can be used to look for sequence similarity and infer homology. - Protein Functional Analysis - InterProScan can be used to search for motifs in your protein sequence. - Proteomic Services NEW - UniProt DAS server allows researchers to show their research results in the context of UniProtKB/Swiss-Prot annotation. - Sequence Analysis - ClustalW2 a sequence alignment tool. - Structural Analysis - MSDfold can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB). - Web Services - provide programmatic access to the various databases and retrieval/analysis services EBI provides. - Tools Miscellaneous - Expression Profiler a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Sponsors: This resource is sponsored by EBI.

Proper citation: Toolbox at the European Bioinformatics Institute (RRID:SCR_002872) Copy   

•   Source: SciCrunch Registry

http://gpcr.biocomp.unibo.it/esldb

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.

Proper citation: eSLDB - eukaryotic Subcellular Localization database (RRID:SCR_000052) Copy   

•   Source: SciCrunch Registry

http://interolog.gersteinlab.org/

Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins.

Proper citation: Interolog/Regulog Database (RRID:SCR_000755) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/cgi-bin/teams/team30/arnie

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.

Proper citation: ARNIE (RRID:SCR_000514) Copy   

•   Source: SciCrunch Registry

http://www.wriwindber.org/wriwindber/Platforms/TissueBanking.aspx

Under the direction of Stella Somiari, Ph.D., the tissue bank at Windber Research Institute acquires and banks large numbers of high quality and well annotated normal and diseased tissue specimens. These specimens are obtained from fully informed and consented donors using Institutional Review Board (IRB) approved protocols and are accompanied by detailed clinical, family history and demographic information. The tissue bank has established Standard Operating Procedures (SOPs) for tissue acquisition, handling, processing, packaging and shipping. All collaborators at participating clinics/medical centers utilize these procedures to ensure that the integrity of the specimen is maintained. Tissue types in our collection include plasma, serum, tissue embedded in optimum cutting temperature (OCT), formalin fixed paraffin embedded, and flash frozen. We also isolate and bank tissue derived products such as DNA, RNA and protein for research. Very stringent SOPs are in place for the process of extraction of these tissue-derived products and for quality control/quality assurance (QA/QC). The WRI tissue bank currently has 5 isothermal freezers each with the capacity to store 36,000 specimens. For all specimens obtained from surgical procedures, routine histology is performed to obtain representative Hematoxylin and Eosin (H & E) stained sections for imaging/archiving. All H & E sections are imaged on the Trestle SL-50 imaging system and these images are available online to designated collaborative sites. A certified pathologist verifies all tissue specimens and WRI has telepathology capabilities, which can also be utilized for pathology verification when a second pathologist opinion is required to confirm specimen diagnosis. Other uses of the telepathology capabilities include the verification of Laser Capture Microdissection (LCM) sections (by pathologist) to ensure the correct areas are captured for research. The telepathology system at WRI is the Trestle Corporation's Medmicro system, which permits the pathologist to remotely view, navigate and share images at sub-micron resolution over standard internet connections in real-time.

Proper citation: Windber Tissue Bank (RRID:SCR_000509) Copy   

•   Source: SciCrunch Registry

http://www.proglycprot.org/

Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time.

Proper citation: ProGlycProt (RRID:SCR_000622) Copy   

•   Source: SciCrunch Registry