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From Protein Structure to Function via Computational Tools and Approaches
Author(s) -
Kolodny Rachel,
Kosloff Mickey
Publication year - 2013
Publication title -
israel journal of chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.908
H-Index - 54
eISSN - 1869-5868
pISSN - 0021-2148
DOI - 10.1002/ijch.201200078
Subject(s) - protein data bank (rcsb pdb) , protein data bank , protein structure database , chemistry , function (biology) , computational biology , protein structure , protein function , protein structure prediction , sequence (biology) , space (punctuation) , theoretical computer science , computer science , biochemistry , microbiology and biotechnology , sequence database , biology , gene , operating system
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.