MolTalk - a programming library for protein structures and structure analysis

Background: Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. Results: We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Wee...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Alexander V. Diemand, Holger Scheib
• Keywords: Analyse Protein, BMCBI 2004, Protein Structure, Smalltalk-based Interpreter Moltalk