Journal
ISRAEL JOURNAL OF CHEMISTRY
Volume 53, Issue 3-4, Pages 147-156Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/ijch.201200078
Keywords
bioinformatics; molecular recognition; protein structures; structure-activity relationships
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The three-dimensional structures of proteins are often considered fundamental for understanding their function. Yet, because of the complexity of protein structure, extracting specific functional information from structures can be a considerable challenge. Here, we present selected approaches and tools that we have developed to study and connect protein sequence, structure, and function spaces. First, we consider a global perspective of structure space and view the protein data bank (PDB) as a database. We highlight challenges in searching protein structure space and in using the PDB as the starting point for computational structural studies. Then we describe a function-oriented view and show examples of how multiple protein structures can be used to extract insights about the function and specificity of proteins at the family level.
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