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http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS

Web service with well defined methods to enable programmatic access to molecular interactions. Standard for computational access to molecular interaction data resources.

Proper citation: PSICQUIC Registry (RRID:SCR_006389) Copy   

•   Source: SciCrunch Registry

http://www.lipidmaps.org/

Multi-institutional supported website and database that provides access to large number of globally used lipidomics resources. Internationally led the field of lipid curation, classification, and nomenclature since 2003. Produces new open-access databases, informatics tools and lipidomics-focused training activities will be generated and made publicly available for researchers studying lipids in health and disease.

Proper citation: LIPID Metabolites And Pathways Strategy (RRID:SCR_006579) Copy   

•   Source: SciCrunch Registry

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

Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries.

Proper citation: InterPro (RRID:SCR_006695) Copy   

•   Source: SciCrunch Registry

http://www.dbmi.pitt.edu/nlpfront

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Repository of de-identified clinical reports available for NLP researchers has been designed. Work with the AMIA NLP working group in designing annotation schemas and obtaining annotations, design a repository for shareable annotations, help design and execute a shared task in IE from clinical reports. The University of Pittsburgh NLP Repository contains clinical reports that are available to the community for NLP research purposes and comprises: # Report Repository - one month of de-identified clinical reports from multiple hospitals and # Annotation Repository - annotations performed on reports from the Report Repository. Anyone performing annotations on reports from the NLP Repository is required to deposit their annotations. The Repository contains reports of the following types generated from multiple hospitals during a single month: * History and Physicals * Progress Notes * Consultation Reports * Radiology Reports * Surgical Pathology Reports * Emergency Department Reports * Discharge Summaries * Operative Reports * Cardiology Reports

Proper citation: Open Clinical Report Repository (RRID:SCR_013585) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ai.sri.com/ptools/

A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks.

Proper citation: Pathway Tools (RRID:SCR_013786) Copy   

•   Source: SciCrunch Registry

https://www.phenix-online.org/

A Python-based software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Phenix includes programs for assessing data quality, experimental phasing, molecular replacement, model building, structure refinement, and validation. It also includes tools for reflection data and creating maps and models. Phenix can also be used for neutron crystallography. Tutorials and examples are available in the documentation tab.

Proper citation: Phenix (RRID:SCR_014224) Copy   

•   Source: SciCrunch Registry

http://fatcat.burnham.org/

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   

•   Source: SciCrunch Registry

http://sift.bii.a-star.edu.sg/

Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.

Proper citation: SIFT (RRID:SCR_012813) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/map3d.html

A scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models such as high resolution EEG, MEG, and ECG.

Proper citation: map3d (RRID:SCR_009628) Copy   

•   Source: SciCrunch Registry

http://www.datamonkey.org/

Web-based suite of phylogenetic analysis tools for use in evolutionary biology. Web application for comparative analysis of sequence alignments using statistical models. Used for analyzing evolutionary signatures in sequence data. Datamonkey 2.0 provides curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application.

Proper citation: Datamonkey (RRID:SCR_010278) Copy   

•   Source: SciCrunch Registry

http://targetscan.org/

Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.

Proper citation: TargetScan (RRID:SCR_010845) Copy   

•   Source: SciCrunch Registry

http://www.topsan.org/

Collect, share, and distribute information about protein three-dimensional structures. It serves as a portal for the scientific community to learn about protein structures solved by SG centers, and also to contribute their expertise in annotating protein function. The premise of the TOPSAN project is that, no matter how much any individual knows about a particular protein, there are other members of the scientific community who know more about certain aspects of the same protein, and that the collective analyses from experts will be far more informative than any local group, let alone individual, could contribute. They believe that, if the members of the biological community are given the opportunity, authorship incentives, and an easy way to contribute their knowledge to the structure annotation, they would do so. Therefore, borrowing elements from successful, distributed, collaborative projects, such as Wikipedia (the free encyclopedia anyone can edit) and from other open source software development projects, TOPSAN will be a broad, collaborative effort to annotate protein structures, initially, those determined at the JCSG. They believe that the annotation of proteins solved by structural genomics consortia offers a unique opportunity to challenge the extant paradigm of how biological data is collected and distributed, and to connect structural genomics and structural biology to the entire biological research community. TOPSAN is designed to be scalable, modular and extensible. Furthermore, it is intended to be immediately useful in a simplistic way and will accommodate incremental improvements to functionality as usage becomes more sophisticated. Their annotation pages will offer the end user a combination of automatically generated as well as expert-curated annotations of protein structures. They will use available technology to increase the speed and granularity of the exchange of scientific ideas, and use incentive mechanisms that will encourage collaborative participation.

Proper citation: TOPSAN (RRID:SCR_005758) Copy   

•   Source: SciCrunch Registry

http://publications.nigms.nih.gov/chemhealth/

Visit ChemHealthWeb for research highlights, chemist profiles, games and videos and other Web extras. The NIGMS Chemistry of Health booklet describes basic chemistry and biochemistry research that spurs a better understanding of human health.

Proper citation: ChemHealthWeb (RRID:SCR_005851) Copy   

•   Source: SciCrunch Registry

http://polbase.neb.com/

Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software.

Proper citation: Polbase (RRID:SCR_006107) Copy   

•   Source: SciCrunch Registry

https://phenome.jax.org/centers/QTLA

Raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive.

Proper citation: QTL Archive (RRID:SCR_006213) Copy   

•   Source: SciCrunch Registry

https://proxl-ms.org/

Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination.

Proper citation: Protein Cross-Linking Database (RRID:SCR_021027) Copy   

•   Source: SciCrunch Registry

http://www.kojak-ms.org/

Software tool for identification of cross-linked peptides from mass spectra. Used for analysis of chemically cross-linked protein complexes. Used to analyze both novel and existing data sets.

Proper citation: Kojak (RRID:SCR_021028) Copy   

•   Source: SciCrunch Registry

https://crispresso.pinellolab.partners.org/submission

Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.

Proper citation: CRISPResso (RRID:SCR_021538) Copy   

•   Source: SciCrunch Registry

https://github.com/nskvir/RepEnrich

Software tool to profile enrichment of next generation sequencing reads at transposable elements. Method to estimate repetitive element enrichment using high throughput sequencing data. Used to study genome wide transcriptional regulation of repetitive elements.RepEnrich2 is updated method to estimate repetitive element enrichment using high-throughput sequencing data.

Proper citation: RepEnrich (RRID:SCR_021733) Copy   

•   Source: SciCrunch Registry

https://midasnetwork.us/covid-19/

Portal for COVID-19 modeling research. Public access data collections with documented metadata.Computational models to study transmission dynamics of broad range of infectious diseases.

Proper citation: Modeling Infectious Disease Agents Study online portal for COVID-19 (RRID:SCR_018281) Copy   

•   Source: SciCrunch Registry