Abstract: In an era that has been dominated by Structural Biology for the last 30-40 years, a dramatic change of focus
towards sequence analysis has spurred the advent of the genome projects and the resultant diverging sequence/structure
deficit. The central challenge of Computational Structural Biology is therefore to rationalize the mass of sequence information
into biochemical and biophysical knowledge and to decipher the structural, functional and evolutionary clues encoded
in the language of biological sequences. In investigating the meaning of sequences, two distinct analytical themes
have emerged: in the first approach, pattern recognition techniques are used to detect similarity between sequences and
hence to infer related structures and functions; in the second ab initio prediction methods are used to deduce 3D structure,
and ultimately to infer function, directly from the linear sequence. In this article, we attempt to provide a critical assessment
of what one may and may not expect from the biological sequences and to identify major issues yet to be resolved.
The presentation is organized under several subtitles like protein sequences, pattern recognition techniques, protein tertiary
structure prediction, membrane protein bioinformatics, human proteome, protein-protein interactions, metabolic networks,
potential drug targets based on simple sequence properties, disordered proteins, the sequence-structure relationship
and chemical logic of protein sequences.