TY - JOUR
T1 - Search similar protein structures with classification, sequence and 3D alignments
AU - Lu, Zaixin
AU - Zhao, Zhiyu
AU - Garcia, Sergio
AU - Krishnaswamy, Krishnakumar
AU - Fu, Bin
N1 - Funding Information:
We are grateful to anonymous referees for their helpful comments. This research was supported by the National Science Foundation Early Career Award 0845376.
PY - 2009
Y1 - 2009
N2 - We have developed an algorithm and web tool to search similar protein structures in the PDB (Protein Data Bank). The algorithm is a combination of a series of methods including protein classification, geometric feature extraction, sequence alignment, and 3D structure alignment. Given a protein structure, the tool can efficiently discover similar structures from hundreds of thousands of structures stored in the PDB. Our experimental results show that it is more accurate than other well-known protein search systems including PSI-BLAST, 3D-BLAST, and SSM in finding proteins that are structurally similar to the query protein, and its speed is also competitive with those systems. The algorithm has been fully implemented and is accessible online at the address, which is supported by a cluster of computers.
AB - We have developed an algorithm and web tool to search similar protein structures in the PDB (Protein Data Bank). The algorithm is a combination of a series of methods including protein classification, geometric feature extraction, sequence alignment, and 3D structure alignment. Given a protein structure, the tool can efficiently discover similar structures from hundreds of thousands of structures stored in the PDB. Our experimental results show that it is more accurate than other well-known protein search systems including PSI-BLAST, 3D-BLAST, and SSM in finding proteins that are structurally similar to the query protein, and its speed is also competitive with those systems. The algorithm has been fully implemented and is accessible online at the address, which is supported by a cluster of computers.
KW - Protein search
KW - Protein structure alignment
UR - http://www.scopus.com/inward/record.url?scp=70349642680&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=70349642680&partnerID=8YFLogxK
U2 - 10.1142/S021972000900431X
DO - 10.1142/S021972000900431X
M3 - Article
C2 - 19785044
AN - SCOPUS:70349642680
SN - 0219-7200
VL - 7
SP - 755
EP - 771
JO - Journal of Bioinformatics and Computational Biology
JF - Journal of Bioinformatics and Computational Biology
IS - 5
ER -