| Destination |
Web Address |
| Metal-MACiE Database |
www.ebi.ac.uk/thornton-srv/databases/Metal_MACiE/home.html |
| Metal-MACiE aims to annotate both the properties and functions of metal ions involved in the reactions of enzymes. |
| CoFactor Database |
www.ebi.ac.uk/thornton-srv/databases/CoFactor |
| CoFactor is a collection of primary literature knowledge and mechanism of organic enzyme cofactors. |
| FunTree |
www.ebi.ac.uk/thornton-srv/databases/FunTree/ |
| FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. |
| PROCOGNATE |
www.ebi.ac.uk/thornton-srv/databases/procognate/ |
| This database contains an assignment of PDB ligands to the domains of structures as classified by the CATH, SCOP and Pfam databases |
| IUBMB Enzyme Nomenclature |
www.chem.qmul.ac.uk/iubmb/enzyme
http://www.enzyme-database.org/ |
| The first address here is the official IUBMB Enzyme Nomenclature website, which includes historical information on the EC code and nomenclature. The second links to ExplorEnz, which is the official IUBMB enzyme nomenclature website. |
| IntEnz |
www.ebi.ac.uk/intenz |
| The Integrated relational Enzyme database is a collaboration with the Swiss Institute of Bioinformatics (SIB) and it is this collaboration that is responsible for the production of the ENZYME resource. IntEnz also incorproates the IUBMB enzyme nomenclature. This is the resource to which MACiE entries link directly. |
| ChEBI |
www.ebi.ac.uk/chebi |
| ChEBI (Chemical Entities of Biological Interest) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. ChEBI encompasses an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. |
| ChEMBL |
www.ebi.ac.uk/chembldb/ |
| ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). |
| The Protein Databank in Europe (PDBe) |
www.ebi.ac.uk/pdbe/ |
| This used to be called the Macromolecular Structures Database (MSD). MACiE links to this, rather than the PDB itself, as this is an EBI view of the PDB. |
| The RCSB Protein Data Bank |
www.rcsb.org/pdb/ |
| The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies |
| PDBSum |
www.ebi.ac.uk/thornton-srv/databases/pdbsum/ |
| PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them. |
| The CATH Database |
http://www.cathdb.info/ |
| CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). |
| IUPAC Compendium of Chemical Terminology |
http://goldbook.iupac.org/ |
| The IUPAC Compendium of Chemical Terminology, also known as the Gold Book, is essentially a dictionary of chemical terminology and the basis of most of the MACiE dictionary terms. |
| The Catalytic Site Atlas |
www.ebi.ac.uk/thornton-srv/databases/CSA/ |
| The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. |
| BRENDA |
www.brenda-enzymes.info |
| This is a database of enzymes, which includes kinetic data, as well as data on inhibitors, activators, cofactors, etc. |
| SABIO-RK |
sabiork.h-its.org/ |
| The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modellers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. |
| KEGG |
www.genome.jp/kegg/ |
| KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database of biological systems, consisting of genetic building blocks of genes and proteins (KEGG GENES), chemical building blocks of both endogenous and exogenous substances (KEGG LIGAND), molecular wiring diagrams of interaction and reaction networks (KEGG PATHWAY), and hierarchies and relationships of various biological objects (KEGG BRITE). KEGG provides a reference knowledge base for linking genomes to biological systems and also to environments by the processes of PATHWAY mapping and BRITE mapping. |
| Structure Function Linkage Database |
sfld.rbvi.ucsf.edu/ |
| The SFLD is a database of enzyme reaction mechanisms, this database focusses on specific superfamilies. MACiE also links to this where there are common PDB codes. |
| EzCatDB |
mbs.cbrc.jp/EzCatDB/ |
| A database of enzyme reaction mechanisms. Similar to MACiE, but has a lower level of detail, also has more entries. MACiE also links to this where there are common PDB codes. |
| Enzyme Structures Database |
www.ebi.ac.uk/thornton-srv/databases/enzymes/ |
| This is very useful for finding PDB codes to go with EC codes |
| PDBbind |
sw16.im.med.umich.edu/databases/pdbbind/index.jsp |
| The PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). All of the binding affinity data compiled in this database are cited from original references. |
| PROSITE |
www.expasy.org/prosite/ |
| PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. |
| Pfam |
pfam.sanger.ac.uk |
| The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). |
| InterPro |
www.ebi.ac.uk/interpro |
| InterPro is an integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. |
| UniProtKB |
www.uniprot.org |
| The mission of UniProt is to provide the scientific community with a comprehensive, high quality and freely accessible resource of protein sequence and functional information. UniProt is comprised of four components, each optimised for different uses. The UniProt Knowledgebase (UniProtKB) is the central access point for extensive curated protein information, including function, classification, and cross-reference. It consists of two sections: UniProtKB/Swiss-Prot which is manually annotated and is reviewed and UniProtKB/TrEMBL which is automatically annotated and is not reviewed. The UniProt Reference Clusters (UniRef) databases provide clustered sets of sequences from the UniProtKB and selected UniProt Archive records to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences. The UniProt Archive (UniParc) is a comprehensive repository, used to keep track of sequences and their identifiers. The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data. |
| dbPTM |
dbptm.mbc.nctu.edu.tw |
| A database of experimentally verified post-translational modifications (PTMs) |
| fireDB - firestar |
firedb.bioinfo.cnio.es/ |
| fireDB is a database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords. firestar predicts functionally important residues based on the fireDB database. |
| MetaCyc |
www.metacyc.org/ |
| MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. |
| Jmol |
jmol.sourceforge.net/ |
| Jmol: an open-source Java viewer for chemical structures in 3D |
| JUMBO Toolkit |
sourceforge.net/projects/cml |
| XML-based tools for using Chemical Markup Language (CML), including XSD XML Schemas for validation, datatyping and constraining CML documents and XSLT Stylesheets for transforming, filtering and rendering. |
