Tag: computational predictions

STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations.

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pf ...

InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as si ...

MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. The database is cross-species and cross-technique and it covers metabolite structures and their reference spectra as well as their biological ro ...

The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, ...

Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs contai ...

The IEDB provides the scientific community with a central repository of freely accessible epitope data and epitope prediction and analysis resources. The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear ...

modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for ide ...

The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and an ...

STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.

The Antimicrobial Peptide Database (APD) contains information on antimicrobial peptides from across a wide taxonomic range. It includes a glossary, nomenclature, classification, information search, prediction, design, and statistics of AMPs. The anti ...

TDR Targets integrates chemical and genomic information and allows users to prioritize targets and compounds to develop and repurpose new drugs and chemical tools for human pathogens. The TDR Target Project was started in 2005 after a call for applic ...

This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction. ELMs, or short linear motifs (SLiMs ...

The SIGnaling Network Open Resource. The core of SIGNOR is a collection of approximately 12,000 manually-annotated causal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are comp ...

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitati ...

This database enables the reliable identification of an individual Interferon Regulated Gene (IRG) or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It also assists in identifying regulatory elements, chromosoma ...

Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. This is a reimplementation at EMBL-EBI of a resource previously host ...

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data ...

The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules. All data is fr ...

The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. The model archive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in ...

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. Benchmarking results are made ...

GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications.

miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mi ...

Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum ...

The Effective database contains pre-calculated predictions of bacterial secreted proteins and of functional secretion systems. Effective bundles various tools to recognize Type III secretion signals, conserved binding sites of Type III chaperones, eu ...

The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic techno ...

The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or t ...

To understand the mechanisms of influenza A viral replication and the host responses, we took the literature-based manual curation approach to construct a comprehensive influenza virus-host respoce map. The infuenza A virus (IAV) comprehensive pathwa ...

GeneProf Data is an open web resource for analysed functional genomics experiments. We have built up a large collection of completely processed RNA-seq and ChIP-seq studies by carefully and transparently reanalysing and annotating high-profile public ...

PMut Data Repository collects predictions of the pathological effect of all possible single amino acid variants on Uniref Human protein sequences. Predictions were prepared using PMut 2017 predictor (2017 version).

ADPriboDB is a database of ADP-ribosylated proteins and their literature-identified ADP-ribosylated residues. The database includes a variety of information for each entry, including any drug treatments performed to obtain the identification of the m ...

Pathway and Annotated-list Gene-signature Electronic Repository (PAGER) is an repository for pathways, annotated-lists, and gene signatures (PAGs) related to human network biology.

DISNOR is a resource that uses a comprehensive collection of disease associated genes, as annotated in DisGeNET, to interrogate SIGNOR (https://signor.uniroma2.it) in order to assemble disease-specific logic networks linking disease associated genes ...

rPredictorDB is a predictive database of secondary structures of individual RNAs and their formatted plots.

R-loop DB is a collection of R-loop forming sequences (RLFS) predicted computationally in the human genome based on quantitative model of RLFS (QmRLFS). The database additionally includes chromosome coordinates and annotation of many hundred thousand ...

For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. The ModelSEED biochemistry database is the foundation of the biochemical data underlyi ...

InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interac ...

PROXiMATE is a database of thermodynamic data for more than 6000 missense mutations in 174 heterodimeric protein-protein complexes, supplemented with interaction network data from STRING database, solvent accessibility, sequence, structural and funct ...

HCVIVdb is a database of published variations observed within the internal ribosome entry site (IRES) of the hepatitis C Virus.

OmicsDB offers an integrated platform for studying biological networks in multiple organisms, as well as accessing gene expression data. By expanding the classic single species databases across species, it is possible to leverage the amount of inform ...

The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcript ...

Chickspress is a gene expression database for chicken tissues. Chickspress incorporates both NCBI and Ensembl gene models and links these gene sets with experimental gene expression data and QTL information. By linking gene models from both NCBI and ...

Gene Prediction File Format (genePred) is a table format commonly used for gene prediction tracks in the Genome Browser. Variations of genePred include standard format, extended format and a format which includes RefSeq genes with gene names.

PMML (Predictive Model Markup Language) uses XML to represent data mining models. The structure of the models is described by an XML Schema. One or more mining models can be contained in a PMML document. A PMML document is an XML document with a root ...

BIOPYDB is a manually-curated database of human cell specific biochemical pathway data. The information within BIOPYDB is primarily extracted from published scientific literature and a selection of databases. The reconstructed pathways contain inform ...