TY - GEN
T1 - An efficient algorithm for matching protein binding sites for protein function prediction
AU - Ellingson, Leif
AU - Zhang, Jinfeng
PY - 2011
Y1 - 2011
N2 - Comparing the binding sites of proteins is effective for predicting protein functions based on their structure information. However, it is still very challenging to predict the binding ligands from the atomic structures of protein binding sites. In this study, we designed a new algorithm based on the iterative closest point (ICP) algorithm. Our algorithm aims to find the maximum number of atoms that can be superposed between two protein binding sites, where any pair of matched superposed atoms has a distance smaller than a given threshold. The search starts from similar tetrahedra between two binding sites obtained from 3D Delaunay triangulation and uses the Hungarian algorithm to find additional matched atoms. We show that our method finds more matched atoms than a leading method. For benchmark data, we use the Tanimoto Index as a similarity measure and the nearest neighbor classifier to achieve a classification performance comparable to the best methods in the literature among those that provide both the common atom set and atom correspondences.
AB - Comparing the binding sites of proteins is effective for predicting protein functions based on their structure information. However, it is still very challenging to predict the binding ligands from the atomic structures of protein binding sites. In this study, we designed a new algorithm based on the iterative closest point (ICP) algorithm. Our algorithm aims to find the maximum number of atoms that can be superposed between two protein binding sites, where any pair of matched superposed atoms has a distance smaller than a given threshold. The search starts from similar tetrahedra between two binding sites obtained from 3D Delaunay triangulation and uses the Hungarian algorithm to find additional matched atoms. We show that our method finds more matched atoms than a leading method. For benchmark data, we use the Tanimoto Index as a similarity measure and the nearest neighbor classifier to achieve a classification performance comparable to the best methods in the literature among those that provide both the common atom set and atom correspondences.
KW - Functional genomics
KW - Protein binding site matching
KW - Protein function prediction
KW - Protein surface matching
KW - Structure genomics
UR - http://www.scopus.com/inward/record.url?scp=84858962229&partnerID=8YFLogxK
U2 - 10.1145/2147805.2147837
DO - 10.1145/2147805.2147837
M3 - Conference contribution
AN - SCOPUS:84858962229
SN - 9781450307963
T3 - 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011
SP - 289
EP - 293
BT - 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011
T2 - 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011
Y2 - 1 August 2011 through 3 August 2011
ER -