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A publicly available compilation of chemical-protein-disease annotation resources that enables the study of systems pharmacology for a small molecule across multiple layers of complexity from molecular to clinical levels. In this third version, ChemProt has been updated to more than 1.7 million compounds with 7.8 million bioactivity measurements for 19,504 proteins. Within ChemProt, it is possible to navigate the chemogenomics space and to link chemically induced target perturbations to diseases and other biological outcomes. Such tools might be of interest for drug discovery, drug safety and also chemical risk assessment. ChemProt 3.0 supports predicting bioactivities on targets and off-targets for new compounds and can assist in the associations to phenotypes and side effects relationships.
The PDBbind database
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Provides a collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB). The PDBbind database supplies a linkage between energetic and structural information of these complexes, that assist researchers for various computational and statistical studies on molecular recognition occurred in biological systems. It informs about experimental binding data for over 10 700 biomolecular complexes in PDB, including more than 8300 protein-ligand complexes and 2400 other types of complexes.
Binding MOAD / Binding Mother of All Databases
Provides high resolution structures from the PDB with ligand annotation and protein classifications. Binding MOAD contains protein-ligand structures relationships with their corresponding experimental binding affinities. It permits users to display the protein-ligand complex, the ligand’s two-dimensional structure and to realize structure-based searching of ligands. This database represents a large collection of well resolved protein crystal structures.
KLIFS / Kinase-Ligand Interaction Fingerprints and Structures database
Revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them. Based on the underlying systematic and consistent protocol all (currently human and mouse) kinase structures and the binding mode of kinase ligands can be directly compared to each other. Moreover, because of the classification of an all-encompassing binding site of 85 residues it is possible to compare the interaction patterns of kinase-inhibitors to each other to, for example, identify crucial interactions determining kinase-inhibitor selectivity.
A resource for protein-chemical interactions. MATADOR differs from other resources such as DrugBank in its inclusion of as many direct and indirect interactions as we could find. In contrast, DrugBank usually contains only the main mode of interaction. The manually annotated list of direct (binding) and indirect interactions between proteins and chemicals was assembled by automated text-mining followed by manual curation. Each interaction contains links to PubMed abstracts or OMIM entries that were used to deduce the interaction.
NBDB / Nucleotide Binding Data Base
Provides profiles of elementary functional loops (EFLs) involved in binding of nucleotide-containing ligands. Each EFL in form of a PSSM (position-specific scoring matrix) profile is complemented with the information on SCOP entities, structural representatives in the PDB, and interactions between EFLs residues and corresponding parts of ligands. A comprehensive set of 249 profiles covers interactions with 24 nucleotide-containing ligands, cofactors and vitamins. You can explore profile interactions with different ligands and their chemical moieties. It is also possible to search for EFLs involved into binding of nucleotide-containing ligands given the protein sequence of interest.
Simplifies data mining for protein–ligand related information. Relibase is an online repository containing several features such as data enhancement and validation, generation of derived knowledge-based data, and a graphical user interface (GUI). It also includes modules allowing users to handle and compare ligand-binding sites (CavBase module), analyze and validate water molecules (WaterBase module), and assign and validate protonation states and hydrogen-bond networks (HydroBase module).
SCORPIO / Structure-Calorimetry of Reported Protein Interactions Online
Provides access to complete sets of thermodynamic data for protein-ligand complexes that have had their structures resolved. SCORPIO contains a wide variety of ligands ranging from natural substrates—carbohydrates, lipids and peptides—to synthetic inhibitors and drugs. It aims to provide ready access to published calorimetric data for the formation of protein–small molecule complexes of known three-dimensional structure.
SInCRe / Structural Interactome Computational Resource
An integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein-protein and protein-small molecule interactions. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics.
NLDB / Natural Ligand DataBase
Offers collected and predicted 3D protein–ligand interactions for the enzymatic reactions of metabolic pathways registered in KEGG. NLDB contains 68,551 natural, 28,441 analog and 64,204 ab initio complexes, for 3248 KEGG reactions in which 1654 enzymes are involved, and also registers 4379 KEGG reactions in which 3291 enzymes without structural information are involved. It has a flexible search function based on various types of keywords, and an enrichment analysis function based on a set of KEGG compound IDs.
Provides a set of validated cognate ligands for domains and protein structures. PROCOGNATE can assist users in creation of test sets for benchmarking, programs, or methods that predict the binding of cognate ligands to proteins. Its list of ligands come from protein data bank (PDB) and is classified as in the CATH, SCOP and Pfam databases. This database offers a cognate-ligand mapping that was created by assigning the binding of the PDB ligands to specific domains in protein structures.
LigASite / LIGand Attachment SITE
A gold-standard dataset of binding sites in 550 proteins of known structures. LigASite consists exclusively of biologically relevant binding sites in proteins for which at least one apo- and one holo-structure are available. The website interface allows users to search the dataset by PDB identifiers, ligand identifiers, protein names or sequence, and to look for structural matches as defined by the CATH homologous superfamilies. The datasets can be downloaded from the website as Schema-validated XML files or comma-separated flat files.
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