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http://www.ebi.ac.uk/goldman-srv/pandit

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website.

Proper citation: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees (RRID:SCR_003321) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/structure

Database of three-dimensional structures of macromolecules that allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships. * Macromolecular structures: The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. It is possible, for example, to find 3D structures for homologs of a protein of interest by following the Related Structure link in an Entrez Protein sequence record. * Conserved domains and protein classification: Conserved domains are functional units within a protein that act as building blocks in molecular evolution and recombine in various arrangements to make proteins with different functions. The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, in addition to NCBI-curated domains that use 3D-structure information explicitly to define domain boundaries and provide insights into sequence/structure/function relationships. * Small molecules and their biological activity: The PubChem project provides information on the biological activities of small molecules and is a component of NIH''''s Molecular Libraries Roadmap Initiative. PubChem includes three databases: PCSubstance, PCBioAssay, and PCCompound. The PubChem data are linked to other data types (illustrated example) in the Entrez system, making it possible, for example, to retrieve information about a compound and then Link to its biological activity data, retrieve 3D protein structures bound to the compound and interactively view their active sites, and find biosystems that include the compound as a component. * Biological Systems: A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. The NCBI BioSystems Database provides centralized access to biological pathways from several source databases and connects the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system. BioSystem records list and categorize components (illustrated example), such as the genes, proteins, and small molecules involved in a biological system. The companion FLink icon FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems.

Proper citation: NCBI Structure (RRID:SCR_004218) Copy   

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http://signalink.org/

An integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes. The multi-layered database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The website allows the interactive exploration of how each signaling protein is regulated. Features * experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; * combines manual curation with large-scale datasets; * provides confidence scores for each interaction; * operates a customizable download page with multiple file formats (e.g., BioPAX, Cytoscape, SBML).

Proper citation: SignaLink (RRID:SCR_003569) Copy   

•   Source: SciCrunch Registry

http://abc.med.cornell.edu/pdzbase

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.A manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. It currently contains 339 experimentally determined protein protein interactions.

Proper citation: PDZBase (RRID:SCR_003568) Copy   

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https://www.marshallscientific.com/Thermo-Scientific-NanoDrop-Lite-Spectrophotometer-p/nd-lite.htm?gad_source=1&gclid=CjwKCAjwr7ayBhAPEiwA6EIGxC4AdYs99Rc3OfymRdYRe515Nl20zJTLlockTfGGn5tWg6qvZRoQNRoCrwcQAvD_BwE

Compact, personal UV-Vis microvolume spectrophotometer that complements the full-featured NanoDrop 2000/2000c and NanoDrop 8000 instruments.

Proper citation: Thermo Scientific NanoDrop Lite Spectrophotometer (RRID:SCR_025369) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/allopathfinder

Software application and code base that allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space. The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins. It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or "walking" of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. They are investigating which residues are likely to participate in allosteric communication pathways. The application is a collection of C++/QT code, suitable for reproducing the computational results of the paper. (PMID 17900617) In addition, they provide input and alignment information to reproduce Figure 3 (a key figure) in the paper. Examples provided will show users how to use AlloPathFinder with other protein families, assumed to exhibit an allosteric communication. To run the application a multiple sequence alignment of representative proteins from the protein family is required along with at least one protein structure.

Proper citation: Allopathfinder (RRID:SCR_002702) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/ProP/

Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.

Proper citation: ProP Server (RRID:SCR_014936) Copy   

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http://mapman.gabipd.org/web/guest/mapman

Software tool that displays large genomics datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other biological processes.

Proper citation: MapMan (RRID:SCR_003543) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/a/blueprint.org/trades/

With Trajectory Directed Ensemble Sampling (TraDES) create large ensembles of high-quality protein structures quickly, ranging from near-native to partially unfolded to intrinsically unfolded. TraDES is a system for directly controlling and sampling protein conformational space. TraDES has been previously used for measuring the vastness of protein conformational space and testing the hypothesis of a brute force solution to the protein folding problem. Over 10 Billion protein structures have been produced by TraDES software in previous distributed computing experiments. The package is comprised of binary executable programs and accessory programs and scripts as well as protein structure data files that map out protein conformational space in a probabilistic way. The main programs are: * trades - generates protein structures following the Trajectory Distribution (see below) * seq2trj - makes Trajectory Distributions from sequences for sampling * str2tr - makes Trajectory Distributions from 3D structures for sampling Trajectory Distributions - Controlling the Sampling of Conformational Space The concept of the trajectory distribution may be new to many protein scientists. A trajectory distribution is simply a map of available conformational space at an amino acid residue. NMR scientists are the primary users of the TraDES package.

Proper citation: TraDES (RRID:SCR_006142) 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://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://www.umr6026.univ-rennes1.fr/english/home/research/basic/software/cobalten

A comprehensive database that gathers all prediction outputs concerning complete prokaryotic proteomes. It is a client-server application, with the server installed and staying at Biogenouest bioinformatics platform, keeping all needed pre-computed genomic data, while the CoBaltDB Client or GUI is a Java application which communicates with the server via web-services. The CoBaltDB Client needs to be downloaded on your computer.

Proper citation: CoBaltDB (RRID:SCR_011970) Copy   

•   Source: SciCrunch Registry

https://circinteractome.nia.nih.gov/

Web tool for exploring circular RNAs and their interacting proteins and microRNAs. Predicts the miRNAs which can potentially target the circRNA.

Proper citation: Circular RNA Interactome (RRID:SCR_016304) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/Q33238

Qubit fluorometer designed to accurately measure DNA, RNA, and protein quantity, and now also RNA integrity and quality. Qubit 4 Fluorometer was re-engineered to enable data transfer via WiFi as well as to run Qubit RNA IQ assay. Qubit 4 Fluorometer and RNA IQ Assay Kit work together to accurately distinguish intact from degraded RNA in two steps.

Proper citation: Invitrogen Qubit 4 Fluorometer with WiFi (RRID:SCR_026883) Copy   

•   Source: SciCrunch Registry

http://sybil.sourceforge.net/

A web-based software package for comparative genomics.

Proper citation: Sybil (RRID:SCR_005593) Copy   

•   Source: SciCrunch Registry

http://braintrap.inf.ed.ac.uk/braintrap/

This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download.

Proper citation: BrainTrap: Fly Brain Protein Trap Database (RRID:SCR_003398) Copy   

•   Source: SciCrunch Registry

https://www.bioptic.com.tw/product/instruments/qsep100-series/qsep100

Standard-sized automated analyzer with its single-channel design, it can run 1~96 samples. Supports various types of applications, including DNA, RNA and protein fragment analyses and high-voltage fast analysis.

Proper citation: BiOptic Qsep100 Bio-Fragment Analyzer (RRID:SCR_026347) Copy   

•   Source: SciCrunch Registry

http://cudasw.sourceforge.net/

CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher

Proper citation: CUDASW++ (RRID:SCR_008862) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/X2K/

Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.

Proper citation: eXpression2Kinases (RRID:SCR_016307) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/sites/batchentrez

Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers.

Proper citation: Batch Entrez (RRID:SCR_016634) Copy   

•   Source: SciCrunch Registry