This database has the positional information in the amino acid motif structure. The information is identified by experiments or sequence analysis (homology search and multiple alignment). We use PROSITE and BLOCKS as amino acid motif databases. PROSITE has motives from experiments, and BLOCKS has motives from both experiments and sequence analysis. We use PDB as the protein structure database and decide the motif position from SEQRES and ATOM sequences. The reason we need SEQRES and ATOM sequences is because those are not matched in some PDB entries.

TMFunction is a database of functional residues in alpha-helical and beta-barrel membrane proteins. Each protein is identified with its name and source alongwith the UniProt code. The protein data bank (PDB) codes are also given for available proteins. Different methods and experimental parameters, for example, affinity, dissociation constant, IC50, activity etc. are given in the database. Further, we have provided the numerical experimental value for each residue (or mutant) in a protein. The experimental data are collected from the literature both by searching the journals as well as with the keyword search at PubMed. In addition, complete reference is given with journal citation and PMID number.

This database extracts this dynamic information from the protein structure being obtained now and is consist of three kinds of sub-database, that is, 1) evolutional structure change, 2) conformation changes by some binding and 3) structural flexibility, which were individually classified respectively.