TY - GEN
T1 - P-binder
T2 - 8th International Symposium on Bioinformatics Research and Applications, ISBRA 2012
AU - Guo, Fei
AU - Li, Shuai Cheng
AU - Wang, Lusheng
PY - 2012
Y1 - 2012
N2 - Determination of binding sites between proteins has a wide range of applications. Understanding energetics and mechanism of complexes remains one of the essential problems in binding site prediction. We develop a system, P-Binder, for identifying binding sites based on structural compatibility, side-chain conformations, amino acid types and contact energies. P-Binder utilizes an enumeration method and side-chain packing program to identify structurally compatible sites. The system reports the sites with the highest ranked configurations, evaluated through a combination of four statistical energy items. We test P-Binder on protein-protein docking Benchmark v4.0. The overall accuracy and coverage are 64.0% and 69.4% for the bound state, and 51.1% and 61.4% for the unbound state. A comparison with some existing techniques shows P-Binder to improve the success rate by at least 12.3%. The system reports improvements in prediction quality, in terms of both accuracy and coverage. The software package is available at http://sites.google.com/site/guofeics/p-binder for non-commercial use. © 2012 Springer-Verlag.
AB - Determination of binding sites between proteins has a wide range of applications. Understanding energetics and mechanism of complexes remains one of the essential problems in binding site prediction. We develop a system, P-Binder, for identifying binding sites based on structural compatibility, side-chain conformations, amino acid types and contact energies. P-Binder utilizes an enumeration method and side-chain packing program to identify structurally compatible sites. The system reports the sites with the highest ranked configurations, evaluated through a combination of four statistical energy items. We test P-Binder on protein-protein docking Benchmark v4.0. The overall accuracy and coverage are 64.0% and 69.4% for the bound state, and 51.1% and 61.4% for the unbound state. A comparison with some existing techniques shows P-Binder to improve the success rate by at least 12.3%. The system reports improvements in prediction quality, in terms of both accuracy and coverage. The software package is available at http://sites.google.com/site/guofeics/p-binder for non-commercial use. © 2012 Springer-Verlag.
KW - binding site prediction
KW - free energy function
KW - Protein-protein interaction
KW - secondary structure
KW - side-chain conformation
UR - https://www.scopus.com/pages/publications/84861170774
UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-84861170774&origin=recordpage
U2 - 10.1007/978-3-642-30191-9_13
DO - 10.1007/978-3-642-30191-9_13
M3 - RGC 32 - Refereed conference paper (with host publication)
SN - 9783642301902
VL - 7292 LNBI
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 127
EP - 138
BT - Bioinformatics Research and Applications
PB - Springer Verlag
Y2 - 21 May 2012 through 23 May 2012
ER -