Identification of domains and domain interface residues in multidomain proteins from graph spectral method. Export

@article{citeulike:833227, abstract = {We present a novel method for the identification of structural domains and domain interface residues in proteins by graph spectral method. This method converts the three-dimensional structure of the protein into a graph by using atomic coordinates from the PDB file. Domain definitions are obtained by constructing either a protein backbone graph or a protein side-chain graph. The graph is constructed based on the interactions between amino acid residues in the three-dimensional structure of the proteins. The spectral parameters of such a graph contain information regarding the domains and subdomains in the protein structure. This is based on the fact that the interactions among amino acids are higher within a domain than across domains. This is evident in the spectra of the protein backbone and the side-chain graphs, thus differentiating the structural domains from one another. Further, residues that occur at the interface of two domains can also be easily identified from the spectra. This method is simple, elegant, and robust. Moreover, a single numeric computation yields both the domain definitions and the interface residues.}, address = {Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.}, author = {Sistla, R. K. and K V, B. and Vishveshwara, S.}, citeulike-article-id = {833227}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.20444}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15789418}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15789418}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/110432865/ABSTRACT}, day = {15}, doi = {10.1002/prot.20444}, issn = {1097-0134}, journal = {Proteins}, keywords = {interaction-site-prediction, proteins-as-graphs}, month = {May}, number = {3}, pages = {616--626}, posted-at = {2007-08-15 17:51:59}, priority = {2}, title = {Identification of domains and domain interface residues in multidomain proteins from graph spectral method.}, url = {http://dx.doi.org/10.1002/prot.20444}, volume = {59}, year = {2005} }

TY - JOUR ID - citeulike:833227 L3 - citeulike-article-id:833227 N2 - We present a novel method for the identification of structural domains and domain interface residues in proteins by graph spectral method. This method converts the three-dimensional structure of the protein into a graph by using atomic coordinates from the PDB file. Domain definitions are obtained by constructing either a protein backbone graph or a protein side-chain graph. The graph is constructed based on the interactions between amino acid residues in the three-dimensional structure of the proteins. The spectral parameters of such a graph contain information regarding the domains and subdomains in the protein structure. This is based on the fact that the interactions among amino acids are higher within a domain than across domains. This is evident in the spectra of the protein backbone and the side-chain graphs, thus differentiating the structural domains from one another. Further, residues that occur at the interface of two domains can also be easily identified from the spectra. This method is simple, elegant, and robust. Moreover, a single numeric computation yields both the domain definitions and the interface residues. IS - 3 JF - Proteins SN - 1097-0134 AD - Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. EP - 626 TI - Identification of domains and domain interface residues in multidomain proteins from graph spectral method. VL - 59 SP - 616 KW - interaction-site-prediction KW - proteins-as-graphs AU - Sistla, RK AU - K V, B AU - Vishveshwara, S PY - 2005/05/15/ UR - http://dx.doi.org/10.1002/prot.20444 ER -