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http://pdbtm.enzim.hu/

Comprehensive and continuously updated transmembrane protein database of the Protein Data Bank (PDB) created by scanning all PDB entries with the TMDET algorithm. Resource for transmembrane proteins and their structures., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PDBTM (RRID:SCR_011962) Copy   

•   Source: SciCrunch Registry

http://model.nmr.ru/preddimer/

Prediction tool to reconstruct putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal alpha-helices.

Proper citation: PREDDIMER (RRID:SCR_011963) Copy   

•   Source: SciCrunch Registry

http://tmdet.enzim.hu/

Web server for the detection of the transmembrane regions of membrane proteins using their 3D structure only.

Proper citation: TMDET (RRID:SCR_011964) Copy   

•   Source: SciCrunch Registry

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

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

Proper citation: BaCelLo (RRID:SCR_011965) Copy   

•   Source: SciCrunch Registry

http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc/

A package of web-servers for predicting subcellular localization of proteins in different organisms.

Proper citation: Cell-PLoc (RRID:SCR_011966) Copy   

•   Source: SciCrunch Registry

http://cello.life.nctu.edu.tw/

A subCELlular LOcalization predictor based on a multi-class support vector machine (SVM) classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. They combine votes from these classifiers and use the jury votes to determine the final assignment.

Proper citation: CELLO (RRID:SCR_011968) Copy   

•   Source: SciCrunch Registry

http://www.syapse.com/

A platform and application suite for bringing together omics and clinical data.

Proper citation: Syapse (RRID:SCR_012023) Copy   

•   Source: SciCrunch Registry

http://www.antibodypedia.com/

Open-access database of antibodies against human proteins developed through collaboration between Antibodypedia AB and the Nature Publishing Group. It aims to provide the scientific community and antibody distributors alike with information on the effectiveness of specific antibodies in specific applications--to help scientists select the right antibody for the right application. Antibodypedia's mission is to promote the functional understanding of the human proteome and expedite analysis of potential biomarkers discovered through clinical efforts. To this end, they have developed an open-access, curated, searchable database containing annotated and scored affinity reagents to aid users in selecting antibodies tailored to specific biological and biomedical assays. They envisage Antibodypedia as a virtual repository of validated antibodies against all human, and ultimately most model-organism, proteins. Such a tool will be exploitable to identify affinity reagents to document protein expression patterns in normal and pathological states and to purify proteins alone and in complex for structural and functional analyses. They hope to promote characterization of the roles and interplay of proteins and complexes in human health and disease. They encourage commercial providers to submit information regarding their inventory of antibodies with links to quality control data. Independent users can submit their own application-specific experimental data using standard validation criteria (supportive or non-supportive) developed with the assistance of an international advisory board recruited from academic research institutions. Users can also comment on specific antibodies without submitting validation data.

Proper citation: Antibodypedia (RRID:SCR_012782) Copy   

•   Source: SciCrunch Registry

http://www.csbio.sjtu.edu.cn/bioinf/euk-multi-2/

Data analysis service for predicting subcellular localization of eukaryotic proteins including those with multiple sites. Euk-mPLoc covers 22 eukaryotic subcellular locations.

Proper citation: Euk-mPLoc (RRID:SCR_011971) Copy   

•   Source: SciCrunch Registry

http://plantgrn.noble.org/psRNATarget/

A plant small RNA target analysis server which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to ?open? secondary structure around miRNA?s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. PsRNATarget is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded miRNAs and transcript sequences; and outputs a comprehensive list of miRNA / target pairs along with the online tools for batch downloading, key word searching and results sorting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: psRNATarget (RRID:SCR_013321) Copy   

•   Source: SciCrunch Registry

http://www.homolog.us/blogs/

A blog on transcriptomics, bioinformatics and computational biology.

Proper citation: Homologus (RRID:SCR_013325) Copy   

•   Source: SciCrunch Registry

http://regrna2.mbc.nctu.edu.tw/

An integrated web server for identifying functional RNA motifs in an input RNA sequence.

Proper citation: RegRNA (RRID:SCR_013207) Copy   

•   Source: SciCrunch Registry

http://methycancer.psych.ac.cn/

Database to study interplay of DNA methylation, gene expression and cancer that hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing. Interconnections between different data types were analyzed and presented. Search tool and graphical MethyView are developed to help users access all the data and data connections and view DNA methylation in context of genomics and genetics data. The search tool and graphical MethyView are developed to help users access all the data and data connections and view DNA methylation in context of genomics and genetics data. As part of the Cancer Epigenomics Project in China, MethyCancer serves as a platform for sharing data and analytical results from the Cancer Genome/Epigenome Project in China with colleagues all over the world.

Proper citation: MethyCancer (RRID:SCR_013399) Copy   

•   Source: SciCrunch Registry

http://genes.mit.edu/GENSCAN.html

Web server for identification of complete gene structures in genomic DNA.Tool for predicting locations and exon-intron structures of genes in genomic sequences from variety of organisms. Used for prediction of complete gene structures in human genomic DNA.

Proper citation: GENSCAN (RRID:SCR_013362) Copy   

•   Source: SciCrunch Registry

http://probalign.njit.edu/probalign/login

Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.

Proper citation: eProbalign (RRID:SCR_013247) Copy   

•   Source: SciCrunch Registry

http://www.antibodylink.org/

An antibody information database where antibodies are organized by the target protein UniProt id.

Proper citation: Antibody Links (RRID:SCR_013251) Copy   

•   Source: SciCrunch Registry

http://www.thegeneticgenealogist.com/

Blog that examines the intersection of traditional genealogical techniques and modern genetic research.

Proper citation: Genetic Genealogist (RRID:SCR_013102) Copy   

•   Source: SciCrunch Registry

http://www.dna.affrc.go.jp/PLACE/

A database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included. Note: As of January 2007, PLACE is no longer updated or maintained.

Proper citation: PLACE- A Database of Plant Cis-acting Regulatory DNA Elements (RRID:SCR_013428) Copy   

•   Source: SciCrunch Registry

https://github.com/stamatak/ExaML

Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers.

Proper citation: Examl (RRID:SCR_016087) Copy   

•   Source: SciCrunch Registry

http://epifactors.autosome.ru/

Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products.

Proper citation: EpiFactors (RRID:SCR_016956) Copy   

•   Source: SciCrunch Registry