Biochemistry: Web Resources

A list of more than 2700 natural and synthetic small molecular entities: atoms, molecules, free radicals, ions, and other chemicals with biological impact. It lists the substance's chemical classification, function, alternate names, structure, a link to KEGG, and the proteins it interacts with.

Phylogenetic classification of proteins encoded in complete genomes

A database maintained by the National Institutes of Health (NIH) which tries to organize all the information available about biomedical sciences. It links together sequences, structures, references, etc

KEGG Kyoto Encyclopedia of Genes and Genomes is a database of the metabolic pathways in different organims. It neatly displays these pathways and the enzymes and metabolites involved in them. It is easiest to use if you enter an EC number for a particular enzyme. To do this, choose SEARCH OBJECTS IN KEGG PATHWAYS from the top table. Enter your EC number and click Exec.

Regular special issue of Nucleic Acids Research features descriptions of new and updated online databases covering various areas of molecular biology.

OMIM is a catalog of human genes and genetic disorders. It is easiest to use if you enter an EC number for a particular enzyme.

The Protein Data Bank (PDB) is a repository for all solved protein structures. It gives coordinates for all atoms and other information about the protein structure.

A wiki that has lots of information about proteins. It is a great place to start learning about a protein. It works somewhat like Wikipedia, except that not all the pages are open for general editing and the pages are edited by people knowlegeable about proteins.

"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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits, control proteins, and helicase domain proteins are also included. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. "

This database is searchable and finds structural information on proteins. It also contains links to other protein structural databases from its homepage. "The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification."-taken from SCOP's mainpage