Tag: small molecule

The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from hu ...

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synth ...

Chemical Entities of Biological Interest (ChEBI) is a free dictionary that describes 'small’ chemical compounds. These compound includes distinct synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions, complexes, conformers, et ...

ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.

The information in the database is presented at two levels: the initial view or landing pages for each target family provide expert-curated overviews of the key properties and selective ligands and tool compounds available. For selected targets more ...

PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More in ...

Established in 1965, the Cambridge Structural Database (CSD) is the a repository for small-molecule organic and metal-organic crystal 3D structures. Database records are automatically checked and manually curated by one of our expert in-house scienti ...

The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information.

The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...

The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

The PeptideAtlas Project provides a publicly-accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. Mass spectrometer output files are collected for human, mouse, yeast, and several other organis ...

PhosphoSite Plus provides extensive information on mammalian post-translational modifications (PTMs). The resource supersedes PhosphoSite a mammalian protein database that provides information about in vivo phosphorylation sites.

MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecu ...

BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scie ...

ConoServer is a database specializing in sequences and structures of peptides expressed by marine cone snails. The database gives access to protein sequences, nucleic acid sequences and structural information on conopeptides. ConoServer's data are fi ...

DIANA-TarBase is a reference database that indexes experimentally-supported microRNA (miRNA) targets. It integrates information on cell-type specific miRNA–gene regulation and includes miRNA-binding locations. The target data provided by DIANA-TarBas ...

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.

Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-ca ...

The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. ...

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 Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, ...

IMGT is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (Ig ...

A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequen ...

The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.

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 ...

The Therapeutic Target Database provides information about therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links ...

Drug-related information: medical indications, adverse drug effects, drug metabolism and Gene Ontology terms of the target proteins.

BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH.

DBETH is the Database of Bacterial Exotoxins for Human. The aim of this database is to assemble information on the toxins responsible for causing bacterial pathogenesis in humans.

Orphanet is a unique resource, gathering and improving knowledge on rare diseases so as to improve the diagnosis, care and treatment of patients with rare diseases. Orphanet aims to provide high-quality information on rare diseases, including ...

SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules.

MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondin ...

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughou ...

The Crystallography Open Database (COD) is a project that aims to gather all available inorganic, metal-organic and small organic molecule structural data in one database.

The Open Provenance Model (OPM) is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. ( ...

CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical c ...

YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 ...

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information ...

Using the MR-Base platform to investigate risk factors and drug targets for thousands of phenotypes | This repository contains the case studies associated with the manuscript "Using the MR-Base platform to investigate risk factors and drug targets fo ...

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.

IMGT/3Dstructure-DB (1,2) is the three-dimensional (3D) structure database of IMGT®, the international ImMunoGenetics information system® (3,4) that is acknowledged as the global reference in immunogenetics and immunoinformatics. IMGT ...

CAMPR3 (Collection of Anti-Microbial Peptides) has been generated to enhance research into AMP families. The collection is compatible with well-known databases such as PubMed and Uniprot with information like sequence, protein definition, accession n ...

The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-ref ...

The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details neces ...

miRNA target prediction and functional annotation

Kinase-Ligand Interaction Fingerprints and Structures database (KLIFS) is a database that revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them. Based on the underlying systematic and c ...

PolymiRTS (Polymorphism in microRNAs and their TargetSites) is a database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational ...

microRNA-mRNA interaction maps

canSAR is an integrated cancer research and drug discovery resource that brings together large-scale data from different disciplines and allows query and exploration to help cancer research and drug discovery.

ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.

MIABE is intended to be used as a guideline which should be consulted prior to the publication of data describing small molecules and their interactions with one or more target molecules. It was developed by representatives of pharmaceutical companie ...

Useful biological numbers

Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.

The LINCS Data Portal provides a unified interface for searching LINCS dataset packages and reagents. LINCS data are being made openly available as a community resource through a series of data releases, so as to enable scientists to address a broad ...

Arabidopsis Protein Phosphorylation Site Database

iProX is a public platform for collecting and sharing raw data, analysis results and metadata obtained from proteomics experiments. The iProX repository employs a web-based proteome data submission process and open sharing of mass spectrometry-based ...

GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.

Function: Rank potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules. The analysis is based on coefficient tables deduced from the published literature.

DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in w ...

The ASTRAL compendium provides a set of tools and databases designed to aid investigators in the analysis of protein structure, particularly through the use of sequence comparison. Astral augments SCOP, a manual classification of protein domains acco ...

ValidatorDB is a collection of validation results for the entire Protein Data Bank. Annotation (3-letter code) of HET residues larger than 6 heavy atoms is inspected, i.e. if the residue has the same topology and stereochemistry as the model ligand o ...

PDBe-KB (Protein Data Bank in Europe - Knowledge Base) is a community-driven resource managed by the PDBe team, collating functional annotations and predictions for structure data in the PDB archive. PDBe-KB is a collaborative effort between PDBe and ...

sORFs.org is a database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are pro ...

FuzDB compiles experimentally observed fuzzy protein complexes, where intrinsic disorder (ID) is maintained upon interacting with a partner (protein, nucleic acid or small molecule) and directly impacts biological function. Entries in the database ha ...

The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.

LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...

DrugCentral is online drug information that provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic mode of action. DrugCentral monitors FDA, EMA, and PMDA for new dr ...

Sequence, structure and activity of protein toxins from spider venom

PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other path ...

A resource for exploring the evolution of protein function through relationships in sequence, structure, phylogeny and function.

The Pocketome is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry describes a site on a protein surface that is invo ...

Type II Toxin-Antitoxin loci in bacteria and archaea

Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.

WALTZ-DB 2.0 is a database for characterizing short peptides for their amyloid fiber-forming capacities. The majority of the data comes from electron microscopy, FTIR and Thioflavin-T experiments done by the Switch lab. Apart from that class of data ...

The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.

Validated NMR structures of proteins and nucleic acids.

Platinum is a manually curated, literature-derived database comprising over 1,000 mutations which for the first time associates experimental information on changes in protein-ligand affinity with the three-dimensional structures of the complex.

The Telomerase Database is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein. The objective of this database is to serve the research community by providing a comprehensive compilation of informa ...

ChannelsDB is a comprehensive and regularly updated resource of channels, pores and tunnels found in biomacromolecules deposited in the Protein Data Bank.

An ontology of drug products and packaged drug products.

Herbal active Ingredients and their Targets

SuperDRUG2, an update of the previous SuperDrug database, is a unique, one-stop resource for approved/marketed drugs, containing more than 4,600 active pharmaceutical ingredients. Drugs are annotated with regulatory details, chemical structures (2D a ...

Dragon Antimicrobial Peptide Database is a manually curated database of known and putative antimicrobial peptides (AMPs). It covers both prokaryotes and eukaryotes organisms.

Cytochrome P450 alleles and drug interactions

SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.

SCRIPDB is a chemical structure database designed to make patent metadata accessible. We index public-domain chemical information contained in U.S. patents, and provide the full patent text, reactions, and relationships described within any individua ...

The Therapeutic Structural Antibody Database tracks all antibody- and nanobody-related therapeutics recognized by the World Health Organisation (WHO), and identifies any corresponding structures in the Structural Antibody Database (SAbDab) with near- ...

Tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for pept ...

The Enzyme Portal is for those interested in the biology of enzymes and proteins with enzymatic activity. It integrates publicly available information about enzymes, such as small-molecule chemistry, biochemical pathways and drug compounds. It contai ...

Chaperonins are a diverse family of molecular chaperones present in the plastids, mitochondria, and cytoplasm of eukaryotes, and in bacteria and archaea. The family is divided into group I (CPN60, also known as Hsp60 or GroEL, found in bacteria, some ...

BitterDB is a free and searchable database of bitter compounds. Compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also conta ...

Reframedb is a comprehensive open-access, drug repositioning screening set of 12,000 compounds that was assembled by combining three widely-used commercial drug competitive intelligence databases (Clarivate Integrity, GVK Excelra GoStar and Citeline ...

Protein-protein and drug-protein interactions for studies of drug repositioning

FerrDb is a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations.

The database of human DNA Methylation and Cancer (MethyCancer) is developed to study interplay of DNA methylation, gene expression and cancer. It hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer informati ...

Antiviral peptides (AVPs) have exhibited huge potential in inhibiting viruses by targeting various stages of their life cycle. Therefore, we have developed AVPdb, available online at http://crdd.osdd.net/servers/avpdb, to provide a dedicated resource ...

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 ...

The KNOTTIN database provides standardized data on the knottin structural family (also referred to as the "Inhibitor Cystine Knot (ICK) motif/family/fold").

Predicted secreted bacterial proteins

Allostery is the most direct and efficient way for regulation of biological macromolecule function induced by the binding of a ligand at an allosteric site topographically distinct from the orthosteric site. Due to the inherent high receptor selectiv ...

VIRsiRNAdb contains information on experimentally validated Viral siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic ...

The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well a ...

Inferred Biomolecular Interaction Server: protein-protein, ligand- and nucleic acid-binding sites

Protein-RNA Interface Database

An Open Access Knowledge Base for Microbial Natural Products Discovery. The Natural Products Atlas Network views of chemical space. The Natural Products Atlas provides a unique tools for exploring natural products chemical space, offering perspecti ...

Mimotope database, active site-mimicking peptides selected from phage-display libraries

nmrshiftdb2 is an NMR database for organic structures and their nuclear magnetic resonance (NMR) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. It also features ...

The Proteomics Informatics Working Group is developing standards for describing the results of identification and quantification processes for proteins, peptides, small molecules and protein modifications from mass spectrometry. This working group is ...

A Database of Hemolytic and Non-hemolytic Peptides

Small nucleolar RNA orthological gene database.

A non-redundant database of protein-peptide complexes

updated data repository of antimicrobial peptides | Browse, Create and Mining Antimicrobial Peptides | 157 new entries are added to in DRAMP. 33 entries are natural AMPs including 31 animal AMPs and 2 plant AMPs. 124 entries are synthetic AMPs | A br ...

Enzymes are nature's catalysts, essential for the chemistry of life. Industrially relevant applications range from food science to laundry. We have now released MACiE, an electronic database of well-characterised enzymatic reactions. MACiE is the res ...

Dictionary on miRNAs and their putative target pathways

CoVex is an interactive online platform for SARS-CoV-2 host interactome exploration and drug (target) identification. CoVex integrates virus-human protein interactions, human protein-protein interactions, and drug-target interactions. It allows visua ...

Cancer-relevant proteins and compound interactions

Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molec ...

Indel Flanking Region Database is an online resource for indels (insertion/deletions) and the flanking regions of proteins in SCOP superfamilies. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid indels, substitut ...

The Ebola and Hemorrhagic Fever Virus Database stems from the Hemorrhagic Fever Viruses (HFV) Database Project founded by Dr. Carla Kuiken in 2009 at the Los Alamos National Laboratory (LANL). The HFV Database was modeled on the Los Alamos HIV Databa ...

The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is an open-access, comprehensive database containing information on amino acid sequences, chemical modifications, 3D structures, bioactivities and toxicities of peptides that p ...

GpDB is a publicly accessible, relational database of G-proteins and their interactions with GPCRs and effector molecules. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive liter ...

RNArchitecture is a database that provides a comprehensive description of relationships between known families of structured ncRNAs, with focus on sequence and structure similarities. RNArchitecture also provides literature information and links to o ...

Protein building blocks for structural analysis, modeling and design

Predicted targets of host and viral miRNAs

Natural and artificial sweetening agents

Thioester-active enzymes

Plant metabolic, regulatory and signaling pathways

Mouse Multiple Tissue Metabolomics Database

Mammal ncRNA-disease repository with increased coverage and annotation. Mammalian ncRNA-Disease Repository. MNDR v3.1: Mammal NcRNA-Disease Repository. MNDR (Mammalian ncRNA-Disease Repository) is a database that curated associations between ncRNA ...

ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together wit ...

DrugCombDB is a comprehensive database dedicated to integrating drug combinations from various data sources, include 1) high-throughput screening assays of drug combinations, 2) external databases, and 3) manual curations from PubMed literature.

The ECM-protein knowledge database. Please follow MatrisomeDB. MatrisomeDB will be hosted at matrisomedb.org very soon.

microRNA Expression and Sequence Analysis Database

Drug2Gene is a free multi-species drug-target knowledge base. It contains integrated and unified data of publicly available relations between drugs/compounds and their gene/protein targets gathered from 20 publicly available bio- and chemoinformatics ...

In silico drug docking against SARS-CoV2 targets

The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies.

A database of proteins undergoing liquid-liquid phase separation in vitro. LLPSDB contains LLPS related proteins together with the corresponding phase separation conditions validated by experiments.

Biomarkers: chemical, protein, chromosomal and genetic

A resource for computational drug design and discovery

Experimentally characterized CAZyme gene clusters

Comparative genomics of Fusarium strains

Coding and non-coding RNA

Experimentally characterized Prokaryotic GlycoProteins

Linear motifs in alpha-helical transmembrane proteins

Japanese Multi Omics Reference Panel

Database of MacroMolecular INteractions

Comprehensive database of fragments linking metabolites, toxic molecules and drugs

Experimentally validated Cell Penetrating Peptides

A database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping | Not a member? Reigist in www.biomarkercenter.org/nglycositeatlas | Database UniProtKB AC/ID Gene Protein Site Peptide Motif Source Year Refer ...

The Lipase Engineering Database (http://www.led.uni-stuttgart.de) integrates information on sequence, structure, and function of lipases, esterases, and related proteins. Sequence data on 806 protein entries are assigned to 38 homologous families, wh ...

A database protal for drug target predictions based knowledge graph embeddings.

SPRITE is a protein structural motif database searching program. Users can upload a PDB file of a query protein structure, and SPRITE compares the input coordinates to a database of 3D side chain arrangements of sites and motifs using a graph theoret ...

FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data.

An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes. R-BIND: The RNA-Targeted BIoactive ligaNd Database. The dataset includes only bioactive ligands with demonstrated activity in cell culture and/or animal models. This ...

An expanded database and web-based tool for structural analysis of DNA-protein complexes. A Database and Web Tool for Structural Analysis of DNA-Protein Complexes. DNAproDB automatically lays out nucleotide and residue interactions maps elegantly. ...

Mycobacterium tuberculosis protein druggability database

Functional annotation of exon skipping event in human. Exon skipping (ES), the most common alternative splicing event, has been reported to contribute to diverse human diseases due to the loss of functional domains sites or frame shifting of open re ...

High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference (RNAi) enables the exploration of genes associated with the phenotype of interest on a large scale. The rapid accumulation of public available genetic screening data provides ...

A database of experimentally supported non-coding RNAs and drug targets in cancer. NoncoRNA (http: www.ncdtcdb.cn:8080 NoncoRNA ) is a manually curated database of experimentally supported non-coding RNAs (ncRNAs) and drug target associations that a ...

The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.

Database for drug repurposing, combination therapy, and replacement therapy.

dbPSP (database of Phosphorylation Sites in Prokaryotes) is an updated resource for annotating protein phosphorylation sites (p-sites) in prokaryotes (bacteria and archaea).

It is a site for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying database ...

The Biological Structure Model Archive (BSM-Arc) aims to collect raw data obtained via in silico methods related to structural biology, such as computationally modeled 3D structures and molecular dynamics trajectories. Since BSM-Arc does not enforce ...

DescribePROT is a database containing annotations of 13 putative structural and functional properties at the amino acid level for ~1.4 million proteins from 83 popular/model organism, to be extended to hundreds of additional organisms. Users can sear ...

StackIL6 is a stacking ensemble model for improving the prediction of IL-6 inducing peptides.

A comprehensive database for target genes of gut microbes and microbial metabolites.

IDSM is an integrated database of small molecules.

DNAzymes i.e. DNA molecules with catalytic activity

Covalent Inhibitor DataBase

Membrane-binding Molecular Recognition Features

Projections of protein functional Sites on Exons

This tool is for understanding the coronavirus proteome and evaluating possible drug targets.

A natural products likeness scorer-web application and database | NaPLeS - Natural Product Likeness Score calculator | NaPLeS is an open source web application based fully on open data. Source and installation instructions are available at GitHub. Pl ...

dbPepNeo is a manually curated database for human tumor neoantigen peptides.

CCSbase is an all-in-one web interface for querying the CCS database and accessing the predictive model to support unknown compound identifications.

CoronaVIR is a Web-Based Platform on Coronavirus Disease-19 to Maintain Predicted Diagnostic, Drug, and Vaccine Candidates.

A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides. More and more evidences have shown that non-coding RNAs (ncRNAs), such as lncRNAs, circRNAs and primary miRNAs, could encode proteins or peptides. ncEP is a ...

An Unbiased Data Set for Machine Learning and Virtual Screening. 15 target sets, 9780 actives,and 407839 inactives from high-confidence PubChem Bioassay data. LIT-PCBA: A dataset for virtual screening and machine learninig.

The Blue Star STING database stores information on the interactions between proteins and other bio macromolecules. Structure descriptors used in the analysis of these interactions are stored in STING DB to aid research primarily into the problems cha ...

Database stores structural, physicochemical and pharmacophoric properties of small molecules. For each compound a single 3D conformer is stored along with over 1600 calculated descriptor values (molecular properties). A very efficient method for uniq ...

Mother of All Databases (MOAD) - Polypharmacology Tools and Their Utility in Drug Repurposing.

Cellinker is a platform of ligand-receptor interactions for intercellular communication analysis.

Disco Cross Docking Benchmark server for automated pose and ranking prediction of ligand binding.

The signal molecules and pathways are classified and illustrated by graphs in this database.

G-quadruplex Ligands Database

GlycoConjugate Ontology (GlycoCoO) as a standard semantic framework to describe and represent glycoconjugate data in RDF.

A comprehensive database and analytical platform to dissect the modification of drugs on lncRNA expression

EPSD (Eukaryotic Phosphorylation Sites Database) is a well-annotated data resource of protein phosphorylation sites in eukaryotes.

ARGminer is a web platform dedicated to the validation of ARGs by using sequence alignment and evidence from multiple sources.

A database of high-resolution MS/MS spectra for lichen metabolites. The Global Natural Product Social Molecular Networking (GNPS) site creates a community for natural product researchers working with mass spectrometry data. MassIVE Datasets : Docum ...

a database for protein-peptide identification based on a hybrid clustering algorithm. PROPEDIA is a database of peptide-protein complexes clusterized in three methodologies: (i) peptide sequences; (ii) structure interface; and (iii) binding sites. P ...

A web resource for dendrimer pharmacokinetics investigation and prediction. Abstract: The development of nanomedicines currently suffers from a lack of efficient tools to predict pharmacokinetic behaviour without relying upon testing in large number ...

a database of carbohydrate-binding proteins. An open access database ready to answer your sweetest queries. Carbohydrate-binding proteins play crucial roles across all viruses and organisms

riboCIRC is a comprehensive database of translatable circRNAs. Translation of circular RNAs (circRNAs) now has drawn increasing attention from researchers due to their emerging roles of the functional peptides encoded by circRNAs as new players invol ...

Curated Protein Aggregation Database (CPAD) is an integrated database which contains information related to amyloidogenic proteins, Aggregation prone regions, aggregation kinetics and structure of proteins relevant to aggregation. Authors are encoura ...

A web application for new bioactive peptides from food protein

Anti-Inflamamtory Compounds Database for drug discovery.

FuncPEP is a database of functional peptides encoded by non-coding RNAs.

A chemical data resource with relational data between natural products and biological sources. NPBS Database of Shanghai Institute of Organic Chemistry.

Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics. New E-Resource for Drug Discovery. Regioselectivity prediction for phase 1 and phase 2 metabolism.

A genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. An on-line source for Mycobacterium abscessus modeled structural proteome. MabeLLINI ...

A new database designed specifically for Lactic Acid Bacteria bacteriocins | Bacteriocins from lactic acid bacteria (LAB) are successfully applied as natural alternatives to food preservation and to antibiotics; however, information on these antimicr ...

Drug-peptide conjugates

Structural Antibody Database

Brainbase is a data management, collaboration and sharing platform for the human neuroscience community. The platform provides private research collaboration workspaces, tools to flexibly organize and track subjects and sessions within studies, valid ...

The FoldamerDB is an open source database of foldamers. Foldamers are molecules which mimics the folding of biological molecules into well defined conformation

A unified and manually curated repertoire of GRIN variants. A CURATED DATABASE FOR GRIN VARIANTS.

DrugRepV is a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses.

An NSF-funded multi-institutional project developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes.

DBAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method on genomic and proteomic data.

The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method. FMODB: The database of quantum mechanical data based on the FMO method.

Consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. The database is a useful platform for researchers studying the underlying mechanism for association among genetic ...

CycloBranch is an open and platform-free software that provide the de novo generation of molecular formulas of unknown compounds in both liquid chromatography/mass spectrometry and mass spectrometry imaging datafiles.

Conserved Unique Peptide Patterns (CUPP) is a approach for sequence analysis employing conserved peptide patterns for determination of similarities between proteins. CUPP performs unsupervised clustering of proteins for formation of protein groups an ...

The structural genomics of histone tail recognition web server is an open access resource that presents within mini articles all publicly available experimental structures of histone tails in complex with human proteins. Each article is composed of i ...

Glycan Microarray Database and Analysis Toolset.

A comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations.

Checkpoint Therapeutic Targets and Modulators Database (CKTTD) for Cancer Immunotherapy is a comprehensive database for checkpoint targets and their modulators in cancer immunotherapy. Immune checkpoints are regulators of the immune system which prev ...

An integrated resource for metalloenzyme-ligand associations | The Metalloenzyme-Ligand Association Database (MeLAD)

KAIKObase is a silkworm genome database.

TANTIGEN 2.0 (Tumor T-cell Antigen Database) is a knowledge base of tumor T cell antigens and epitopes.

PepTherDia is a database and tool for structural composition analysis of approved peptide therapeutics and diagnostics. Manually curated database containing a searchable list of approved peptide drugs and diagnostic agents. On these compounds, we hav ...

Avian Immunome DB is a user-friendly interface for extracting genetic information about the avian immune system. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes.

an integrated resource for glycosyltransferase sequences and annotations. Glycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natu ...

A Web Server and Interactive Web Repository of Small Ligand-Protein Binding Sites for Drug Design.

A comprehensive mitochondrial toxicity database.

A Comprehensive Database for Association Between Microbiota and Disease.

Facilitating drug discovery with enriched comparative data of targeted agents.

Protein-Nucleic Acid Binding Energetic Database

Human 51 672 molecular pathways database with tools for activity calculating and visualization.

Database to integrate, analyze and visualize human disease-related circRNA transcriptome.

A large-scaled depository of mass spectrometry datasets for metabolome analysis.

B3Pdb: a database of blood-brain barrier-penetrating peptides.

CMBD (Cancer Metabolic Biomarker knowledge Database) a manually curated cancer metabolic biomarker knowledge database.

CrustyBase is an interactive online database for crustacean transcriptomes. CrustyBase provides an environment for navigating and visualising crustacean transcriptome datasets. Users can search existing transcriptomes or import new datasets of their ...

a manually curated database of lysosomal enzymes associated with rare diseases. RareLSD: Database for Human Lysosomal Enzymes. RareLSD: A Database for Human Lysosomal Enzymes. RareLSD is a manually curated database of 63 lysosomal enzymes present i ...

a database of promiscuous proteins. Promiscuous behaviour in proteins and enzymes remains a challenging feature to understand the structure-function relationship. Here we present ProtMiscuity, a manually curated online database of proteins showing c ...

Human kinase pocket database for drug design. BACKGROUND:The kinase pocket structural information is important for drug discovery targeting cancer or other diseases. Although some kinase sequence, structure or drug databases have been developed, the ...

A Manually Curated Database Dedicated to Hybrid Molecules for Chemical Biology and Drug Discovery | Hybrid Molecules is defined as the design of new chemical molecule that hybridizes two or more pharmacophoric moieties from known identical or non-ide ...

A Comprehensive Database for Drug Repositioning Inspired by Experimental Knowledge | Drug Repositioning Drug repositioning, or the identification of new indications for approved therapeutic drugs, has gained substantial traction with both academics a ...

Antibody high-density alignment visualization and analysis platform with an integrated database.

A software designed for the analysis of binding curves with which to evaluate the interactions of biomolecules.

A Comprehensive Resource for Genetic Targets in Immune-Mediated Disease

A Comprehensive Resource for Targeted Proteomics Assays in the Community.

Sequence composition dynamics of genes and genomes.

An integrative database of quantitative post-translational modifications in plants.

A Protein Data Bank extension database of pKa and pI theoretical values

A knowledgebase of human long non-coding RNAs with enhanced curation model and database system.

The SistematX Web Portal of Natural Products is database of secondary metabolites.

Database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale.

A database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses.

Database for the mulberry metabolome. The Mulberry Metabolome Database. Comprehensively, freely, and User-friendly.

DenvInD is a database containing dengue virus inhibitors for clinical and molecular research.

Automatization and self-maintenance of the O-GlcNAcome catalog.

Toward Enhancing the Precision of Top Hits in Ligand-Based Virtual Screening of Drug Leads from Large Compound Databases.

SAPdb (Self Assembling Peptides Database) is a database of short peptides and the corresponding nanostructures formed by self-assembly.

An intuitive database of RNA pocket topology information with RNA-ligand data resources.

FermFooDb is a database of peptides derived from fermented foods contains 2325 entries of unique peptides from the fermented foods.

The evolutionary history of topological variations in the CPA/AT transporters. Structural models, topology information and other details are presented in a searchable database, CPAfold

The Glycine Receptor Allosteric Ligands Library (GRALL). GRALL – [IFM] LABORATOIRE D’INGÉNIERIE DES FONCTIONS MOLÉCULAIRES.

ZINClick is a virtual combinatorial database of over 16 million of 1,4-disubstituted-1,2,3-triazoles (Molecular Weight < 1000), each can be easily synthesized and it is at the same time new and patentable!

TUPDB (Target-Unrelated Peptide Data Bank) is a comprehensive database of target-unrelated peptides (TUPs) and TUP motifs. It contains extensive information extracted from research articles and public databases.

new binding kinetics database and its integration in an open-source binding analysis software. Kinetics OF Featured Interactions. KOFFI-DB (???) is an article based database for kinetic constants of biomolecular interactions. We focused on interact ...

SYNBIP is a SBP database that UNIQUE in (a) comprehensively describing thousands of SBPs from the perspectives of scaffolds, biophysical & functional properties, etc.; (b) panoramically illustrating the binding targets & the broad application of each ...

Database for skin permeation of xenobiotics. Jupyter Notebook which leads through the code used to create huskinDB publication Figures. huskinDB is a human skin permeation database containing information on experimental protocols used. It provides ...

The One-stop Database for COVID-19 Specific Humoral Immunity and Clinical Parameters.

The Automated Topology Builder (ATB) and Repository is intended to facilitate the development of molecular force fields for Molecular Dynamics or Monte Carlo simulations of biomolecular systems. Applications include the study of biomolecule:ligand co ...

The NP-MRD is a freely available cloud-based, user-friendly, FAIR electronic database. NP-MRD accepts NMR data and associated metadata from newly undertaken NP studies.

NICEdrug.ch is a resource allowing systematic and large-scale computational analysis of drug biochemistry (metabolic precursors or prodrugs and metabolic fate or degradation), enzymatic targets, and toxicity in the context of cellular metabolism, i.e ...

A database for improving the rational design of glucose-tolerant β-glucosidases. A database of mutant β-glucosidases. Glutantbase is a database, webtool and method to evaluate mutations for β-glucosidases proteins used in industrial applications. G ...

MolMeDB is an open chemistry database concerning the interaction of molecules with membranes.

PSnpBind is a large database of protein–ligand complexes covering a wide range of binding pocket mutations and small molecules’ landscape. This database can be used as a source of data for different types of studies, for example, developing machine l ...

Experimental coronavirus protein structures

Database of commercially-available compounds for virtual screening and chemoinformatics

A database of quorum-sensing peptides

DSDBASE is a database of disulphide bonds in proteins that provides information on native disulphides and those that are stereochemically possible between pairs of residues for all known protein structural entries. The modelling of disulphides has be ...

ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG). This knowledge environment includes ...

Metal binding sites, antigen epitopes, and drug binding sites are viral protein hotspots that control how viruses interact with their hosts. Like Google maps organizes and annotates points of interest on the planet, virus-M-E-D (Metal binding sites, ...

Het-PDB Navi is a database that collects small molecules found in Protein Data Bank (PDB). An atomic reality of protein function is based on interactions between a protein and another molecule. One of the approaches to assume protein functions from t ...

RESP and ESP atomic charges and force field libraries for small molecules and molecular fragments

A comprehensive database of toxic compounds

Microbial Volatile Organic Compounds

Database of flavors and scents

Tool to prioritize therapeutic vulnerabilities in cancer.

An endogenous peptide database.

SPENCER is a catalog of small peptides encoded by ncRNAs. The ncRNA encoding peptides were derived from re-annotation of public mass spectrometry data from over 1,700 patient samples spanning diverse cancers. SPENCER enables the users to simply and c ...

Docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases.

COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download ntural products (NPs). NPs are small molecules prod ...

A Crowd-Sourced, Natural Product Screening Library for Exploring Biological Space.

An integrated omics database for functional genomic analysis of cyanobacteria.

A curated database of molecular tastants.

T1TAdb is a database of Type I Toxin-Antitoxin systems.

Enhanced biochemical coverage for peak identification in untargeted metabolomics.

A database of ribozymes.

A comprehensive and curated portal for translational research.

PDB-Ligand is a three dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). One unique feature of PDB-Ligand is that one can browse, classify, superimpose, and visual ...

RNA aptamer 3D-structural modeling database.

Database of HIV Amino Acid Sequences and Clinical Data of Infected Patients.

A database of potential ligand binding sites in the human proteome.

Knowledgebase of Microbes’ Battling Agents for Therapeutics.

Human microbiome affect the host epigenome.

Advanced Functions Embedded in the Second Version of Database, Global Evaluation of SARS-CoV-2/hCoV-19 Sequences 2.

Pathway analysis database of drug response based on phosphorylation activity measurements.

A database for anti-cancer compounds with targets and side effect profiles.

An integrative platform to navigate the biology, structure and chemical inhibition of human proteins.

A database for cancer A-to-I RNA editing with interactive analysis.

HORDB a comprehensive database of peptide hormones.

A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes.

Web-Based Database and Predictor of Anti-Inflammatory Natural Products.

A large and continuously updated drug combination database.

A Database Extension to Visualize Structural Interactome in One-to-many Manner

A high-throughput database of macromolecular host-pathogen interactions on the Web.

A centralized datasource for all data relevant for the understanding of viral fusion peptides.

COVIEdb is a database for potential immune epitopes of coronaviruses.

HIC-Up ("Hetero-compound Information Centre - Uppsala") is a repository of structure-related information about the small molecules (ligands, co-factors, ions, metal-clusters, etc.) that occur in complex with larger biomolecules in any of the structur ...

A library of peptide-based cancer vaccines and their clinical attributes, named CancerVaccine

DisEnrich—the database of human proteome IDRs that are significantly enriched in particular amino acids.

CompoundDB4j is an Integrated Drug Resource of Heterogeneous Chemical Databases.

A Database of Experimentally Identified O-GlcNAc Sites and Proteins.

Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction.

Mine bacterial (meta-)genomic DNA for bacteriocins and RiPPs. Additionally it provides databases and a BLAST against the core peptide databases.

CFM is a database of experimentally validated protocols for chemical compound-based direct reprogramming and transdifferentiation.

A rare skin disease database to link drugs with potential drug targets for rare skin diseases.

The Brazilian Compound Library (BraCoLi) a repository of chemical and biological information for drug design.

AlnC is an extensive database of long non-coding RNAs in Angiosperms.

D3PM is a Comprehensive Database for Protein Motions Ranging from Residue to Domain

A database of food-derived bioactive peptides (DFBP), containing a total of 6276 peptide entries in 31 types from different sources.

An integrative data portal for broad-spectrum antivirals (BSA) and BSA-containing drug combinations (BCCs).

Cancer Antigens Database (CAD) designed to facilitate users to perform a complete exploration of cancer antigens online.

A comprehensive web-based tool to access and analyze glia secretome data. Gliome Database has the following feature regarding glia-secreted proteins.

Compilation, curation and exploration of a knowledgebase of environmental neurotoxicants specific to mammals. Neurotoxicants are an important class of hazardous chemicals.

MetAMDB is a software/database for the analysis of metabolic models and specifically the work with atom mappings.

DrugSimDB is a comprehensive database of multi-modal drug similarity measures by integrating variety of heterogenous datasets.

An RNA-Protein Intuitive Database with RNA Pocket Topology Resources.

A comprehensive database for human proteome repeats. Human Proteome Repeats Database. HPREP : HUMAN PROTEOME REPEATS.

Surface Plasmon Resonance Database (SPRD) is a surface plasmon resonance database of common factors for better experimental planning.

DbRUSP is an interactive database for the analysis and interpretation of newborn screening (NBS) data and for studying the effects of covariates on blood metabolite levels.

ACovPepDB is a comprehensive peptides database of anti-coronavirus peptides, which contains 518 enrties with 214 unique ACovPs manually extracted from research articles and public databases.

FRCD (Food Risk Component Database) is a comprehensive food risk component database with molecular scaffold, chemical diversity, toxicity, and biodegradability analysis.

CovPDB, a database solely dedicated to high-resolution cocrystal structures of biologically relevant cP–L complexes, curated from the Protein Data Bank

ATLASx is a computational map for the exploration of biochemical space ATLASx databases explore potential biochemical reactions within different chemical scopes: bioDB, bioATLAS, and chemATLAS.

The Contraceptive and Infertility Target DataBase. The CITDBase is a tool that provides a gateway for reproductive tissue-specific genes and proteins for research and the discovery of new contraceptive/infertility targets.

A comprehensive database for translatable lncRNAs ( TransLnc) extends immunopeptidome. TransLnc provides both computationally predicted and experimentally supported lncRNA peptides in multiple species.

A database of polar amylodogenic peptides from disordered proteins.

Exposome of Human Milk across India (ExHuMId) is a curated resource and analysis of exposome of human milk across India.

COVID-19 Knowledge Extractor (COKE) is a tool and a web portal to extract drug - target protein associations from the CORD-19 corpus of scientific publications on COVID-19.

DNMSO is an ontology for representing de novo sequencing results from Tandem-MS data. For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and as such drives proteomics.

The Lung Cancer Metabolome Database (LCMD), a freely available online database depositing 2013 lung cancer-related metabolites identified from 65 mass spectrometry-based lung cancer metabolomics studies.

virusMS is a database for synthetic peptides of viruses with mass spectrometry. It is a tool for resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies.

A renovated knowledgebase for deriving biological and chemical insight from genes, proteins, and metabolites.

United States Swine Pathogen Database is integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine.

GPCRmd uncovers the dynamics of the 3D-GPCRome. The online resource for GPCR simulations. GPCRmd is an online platform with web-based visualization capabilities and a comprehensive analysis toolbox that allows scientists from any discipline to visu ...

ConoMode is a database dedicated to collection of the complex 3D structures of conopeptides binding with their target proteins.

Mining drug-target and drug-adverse drug reaction databases to identify target-adverse drug reaction relationships.

The ReACH registry collected clinical information from 51 pediatric ACH patients during its six years of existence, corresponding to ~ 60% of ACH patients aged 3 months to 14 years that were anticipated to live in the Czechia and Slovak Republic

Integrated large scale dataset facilitating Big Data analysis in chemogenomics.

CASTLE (Computational Analysis of SynThetic LEthals) is a collection of synthetic lethal data for various pathogenic organisms, generated computationally. Here, you can find synthetic lethal genes and reactions for more than 70 organisms.

An Expanded Database of Ecological and Phenotypical Features of Microbes. Microbial communities are an incredibly fascinating and genetically diverse set of organisms that live with us, in us, and around us! Explore them all using the Microbe Direct ...

A curated database for binding affinity and neutralization profiles of coronavirus related antibodies.

A user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides.

The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters.

An online tool for designing highly efficient sgRNAs targeting cell surface proteins

KinaFrag is an integrated database to explore the kinase-ligand fragment interaction space. KinaFrag explores the kinase-ligand fragment interaction space for selective kinase inhibitor discovery.

Ebolabase is a comprehensive source for ebola-human interactions has been developed. Ebolabase contains experimentally verified entries of ebola-human interactions. The interactions are visualized as network images. This study provides the informatio ...

OlfactionBase is a manually-curated comprehensive database that incorporates multidimensional facets of major components involved in the olfaction process, i.e., odors, chemicals (both odorants and odourless), Olfactory Receptors (ORs), odorant-OR in ...

The database revolves around the protein structure of catalytic PDE domains and the way PDE inhibitors can interact with them. It contains a systematic analysis of all phosphodiesterase (PDE) catalytic domain crystal structures present in the Protein ...

B-AMP is an Antimicrobial Peptide (AMP) repository for biofilms, consisting of a vast library of 5544 structural AMP models, AMPs annotated to relevant biofilm literature, and protein-peptide interaction models with potential biofilm targets.

DCABM-TCM is a Database of Constituents Absorbed into Blood and Metabolites of Traditional Chinese Medicine.

Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs. Abstract Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular processes. However, discovering s ...

ArVirInd is a knowledge-base of Arbo-Viral proteins from India and its neighbourhood. his is a annotated database, which acts as a repository of Protein sequences for arbo-viruses along with antigenic information. Users can search for protein sequenc ...

A web-based chemical repository of flavonoid compounds. Flavonoids are richly diverse polyphenolic plant secondary metabolites that are known to be crucial component of human diet. These compounds are attributed with variety of nutritional as well a ...

The database contains approximately 2500 3D-structures of active ingredients of essential marketed drugs. For selection purposes and for correlation of structural similarity with medical application, the assignment of the Anatomical Therapeutic Chemi ...

mzCloud is an extensively curated database of high-resolution tandem mass spectra that are arranged into spectral trees. MS/MS and multi-stage MSn spectra were acquired at various collision energies, precursor m/z, and isolation widths using Collisio ...

Protein-gene Expression Nexus (PEN), which consolidates an extensive dataset of paired proteomics and genomics studies. PEN present a database that allows researchers to easily and extensively visualize and annotate changes such as somatic copy numbe ...

Plant cytochrome P450 database and web-based tools for structural construction and ligand docking. It is a reliable template-based structure prediction method (PCPCM), and predicted the structures of 180 plant P450s with known functions. In addition, ...

A comprehensive database on adverse drug events. MetaADEDB is an online database we developed to integrate comprehensive information of adverse drug events (ADEs). The new version consists of 744,709 drug-ADE associations between 8,498 compounds (i ...

Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products. decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER). Alexander M. Kloosterman, Peter Cimermancic, Somayah S. Elsayed, Chao ...

Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies. The METATRYP software consists of:. METATRYP allows users to investigate the occurrence of tryptic peptides within the protein coding sequen ...

A curated natural product database specific to secondary metabolites of medicinal fungi. Medicinal Fungi Secondary metabolites And Therapeutics. MeFSAT (Medicnal Fungi Secondary metabolites and Therapeutics). Medicinal Fungi Secondary Metabolite A ...

A database of exclusive proteins from Leishmania parasite. Leishmania Exclusive Protein Database. The Leishmania Exclusive Protein database (Leish-ExP) is a repository of protein sequences specific to five Leishmania species and genus. Leishmania i ...

Database of amino acid distances in proteins and web application for statistical review of distances. Three-dimensional structure of a protein chain is determined by its amino acid interactions. One approach to the analysis of amino acid interaction ...

The HLA Ligand Atlas. A resource of natural HLA ligands presented on benign tissues | The HLA Ligand Atlas is a comprehensive, tissue and HLA allele specific collection of HLA ligands, generated from more than 1,000 MS experiments | This website uses ...

A Comprehensive Database for Biased GPCR Ligands | A manually curated database of biased GPCR ligands | BiasDB[1] is a manually curated database containing all published biased GPCR ligands. BiasDB currently contains 615 bias cases of signaling bias ...

Automated annotation of amino acid biosynthesis | Abstract GapMind is a web-based tool for annotating amino acid biosynthesis in bacteria and archaea ( http: papers.genomics.lbl gov gaps ). GapMind incorporates many variant pathways and 130 different ...