TY - GEN
T1 - Protein docking with information on evolutionary conserved interfaces
AU - Hashmi, Irina
AU - Akbal-Delibas, Bahar
AU - Haspel, Nurit
AU - Shehu, Amarda
PY - 2011
Y1 - 2011
N2 - Structural modeling of molecular assemblies lies at the heart of understanding molecular interactions and biological function. We present a method for docking protein molecules and elucidating native-like structures of protein dimers. Our method is based on geometric hashing to ensure the feasibility of searching the combined conformational space of dimeric structures. The search space is narrowed by focusing the sought rigid-body transformations around surface areas with evolutionary-conserved amino-acids. Recent analysis of protein assemblies reveals that many functional interfaces are significantly conserved throughout evolution. We test our method on a broad list of sixteen diverse protein dimers and compare the structures found to have lowest lRMSD to the known native dimeric structures to those reported by other groups. Our results show that focusing the search around evolutionary-conserved interfaces results in lower lRMSDs.
AB - Structural modeling of molecular assemblies lies at the heart of understanding molecular interactions and biological function. We present a method for docking protein molecules and elucidating native-like structures of protein dimers. Our method is based on geometric hashing to ensure the feasibility of searching the combined conformational space of dimeric structures. The search space is narrowed by focusing the sought rigid-body transformations around surface areas with evolutionary-conserved amino-acids. Recent analysis of protein assemblies reveals that many functional interfaces are significantly conserved throughout evolution. We test our method on a broad list of sixteen diverse protein dimers and compare the structures found to have lowest lRMSD to the known native dimeric structures to those reported by other groups. Our results show that focusing the search around evolutionary-conserved interfaces results in lower lRMSDs.
KW - evolutionary conservation
KW - evolutionary trace
KW - geometric hashing
KW - protein docking
KW - rigid-body transformations
UR - https://www.scopus.com/pages/publications/84856003207
UR - https://www.scopus.com/pages/publications/84856003207#tab=citedBy
U2 - 10.1109/BIBMW.2011.6112399
DO - 10.1109/BIBMW.2011.6112399
M3 - Conference contribution
AN - SCOPUS:84856003207
SN - 9781457716133
T3 - 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
SP - 358
EP - 365
BT - 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
T2 - 2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
Y2 - 12 November 2011 through 15 November 2011
ER -