iMolTalk: an interactive, internet-based protein structure analysis server

Abstract

IMolTalk (http://i.moltalk.org) is a new and interactive web server for protein structure analysis. It addresses the need to identify and highlight biochemically important regions in protein structures. As input, the server requires only the four-digit Protein Data Bank (PDB) identifier, of an experimentally determined structure or a structure file in PDB format stemming e.g. from comparative modelling. iMolTalk offers a wide range of implemented tools (i) to extract general information from PDB files, such as generic header information or the sequence derived from three-dimensional co-ordinates; (ii) to map corresponding residues from sequence to structure; (iii) to search for contacts of residues (amino or nucleic acids) or heterogeneous groups to the protein, present cofactors and substrates; and (iv) to identify protein–protein interfaces between chains in a structure. The server provides results as user-friendly two-dimensional graphical representations and in textual format, ideal for further processing. At any time during the analysis, the user can choose, for the following step, from the set of implemented tools or submit his/her own script to the server to extend the functionality of iMolTalk.