Proteins: sequence to structure and function--current status.
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.
Shenoy
Sandhya R
SR
Department of Chemistry & Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110 016, India.
Jayaram
B
B
D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D003198:Computer Simulation; D015195:Drug Design; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D008958:Models, Molecular; D010363:Pattern Recognition, Automated; D011487:Protein Conformation; D017510:Protein Folding; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D020543:Proteome / Q000032:analysis; D040681:Structural Homology, Protein
D008565:Membrane Proteins; D011506:Proteins; D020543:Proteome