Janusz M. Bujnicki - Böcker

The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization. Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions, and docking of complexes are put in the context of predicting gene ontology (biological process, molecular function, and cellular component) and discussed in the light of their contribution to the emerging field of systems biology. Topics covered include: first steps of protein sequence analysis and structure predictionautomated prediction of protein function from sequencetemplate-based prediction of three-dimensional protein structures: fold-recognition and comparative modellingtemplate-free prediction of three-dimensional protein structuresquality assessment of protein modelsprediction of molecular interactions: from small ligands to large protein complexesmacromolecular dockingintegrating prediction of structure, function, and interactionsPrediction of Protein Structures, Functions and Interactions focuses on the methods that have performed well in CASPs, and which are constantly developed and maintained, and are freely available to academic researchers either as web servers or programs for local installation. It is an essential guide to the newest, best methods for prediction of protein structure and functions, for researchers and advanced students working in structural bioinformatics, protein chemistry, structural biology and drug discovery.

The book is unique in that it bridges the gap between bioinformaticists and molecular biologists, i.e. the developers and the users of computational methods for biological data analysis and in that it presents examples of practical applications of the bioinformatics tools in the "daily practice" of an experimental research scientist. The book starts with reviews on computational methods for protein sequence-structure-function analysis (sequence studies, structure prediction), followed by methods that explicitly utilize experimental data routinely obtained in the laboratory to improve the functional predictions.The second part comprises a series of examples on how particular applications of different types of bioinformatics methods in combination with experimental studies to validate the hypotheses have led to important scientific discoveries. Therefore, the book is a guide to application of bioinformatics methods in molecular biology, addressed mainly to the research scientists, postdocs, and advanced graduate students.