TY - GEN
T1 - Rapid and accurate protein side chain prediction with local backbone information
AU - Zhang, Jing
AU - Gao, Xin
AU - Xu, Jinbo
AU - Li, Ming
PY - 2008
Y1 - 2008
N2 - High-accuracy protein structure modeling demands accurate and very fast side chain prediction since such a procedure must be repeatedly called at each step of structure refinement. Many known side chain prediction programs, such as SCWRL and TreePack, depend on the philosophy that global information and pairwise energy function must be used to achieve high accuracy. These programs are too slow to be used in the case when side chain packing has to be used thousands of times, such as protein structure refinement and protein design. We present an unexpected study that local backbone information can determine side chain conformations accurately. LocalPack, our side chain packing program which is based on only local information, achieves equal accuracy as SCWRL and TreePack, yet runs 4-14 times faster, hence providing a key missing piece in our efforts to high-accuracy protein structure modeling.
AB - High-accuracy protein structure modeling demands accurate and very fast side chain prediction since such a procedure must be repeatedly called at each step of structure refinement. Many known side chain prediction programs, such as SCWRL and TreePack, depend on the philosophy that global information and pairwise energy function must be used to achieve high accuracy. These programs are too slow to be used in the case when side chain packing has to be used thousands of times, such as protein structure refinement and protein design. We present an unexpected study that local backbone information can determine side chain conformations accurately. LocalPack, our side chain packing program which is based on only local information, achieves equal accuracy as SCWRL and TreePack, yet runs 4-14 times faster, hence providing a key missing piece in our efforts to high-accuracy protein structure modeling.
KW - Local backbone features
KW - Multiclass Support vector machines
KW - Side chain prediction
UR - http://www.scopus.com/inward/record.url?scp=47249099476&partnerID=8YFLogxK
U2 - 10.1007/978-3-540-78839-3_25
DO - 10.1007/978-3-540-78839-3_25
M3 - Conference contribution
AN - SCOPUS:47249099476
SN - 3540788387
SN - 9783540788386
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 285
EP - 299
BT - Research in Computational Molecular Biology - 12th Annual International Conference, RECOMB 2008, Proceedings
T2 - "12th Annual InternationalConference on REsearch in COmputational Molecular Biology, RECOMB 2008"
Y2 - 30 March 2008 through 2 April 2008
ER -