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BIBE
2010
IEEE

Knowledge-Guided Docking of Flexible Ligands to SH2 Domain Proteins

13 years 4 months ago
Knowledge-Guided Docking of Flexible Ligands to SH2 Domain Proteins
Studies of interactions between protein domains and ligands are important in many aspects such as cellular signaling and regulation. In this work, we applied a three-stage knowledgeguided approach of docking flexible peptide ligands to SH2 domains. The first stage of the approach search for binding pockets of SH2 domain proteins and binding motifs of peptide ligands based on known features. The knowledge of the binding sites are used in the second stage as binding constraints to align ligand's peptide backbone to the SH2 domain. The backbonealigned ligands produced serve as good starting points to the third stage which uses a Monte Carlo method to perform the flexible docking. The experimental results show that the backbone alignment method at the second stage produces good backbone conformations which are close to the conformation in complex. The binding site information is well utilized to provide a better starting point to the next docking stage. The subsequent docking is succe...
Haiyun Lu, Shamima Banu Bte Sm Rashid, Hao Li, Wee
Added 08 Nov 2010
Updated 08 Nov 2010
Type Conference
Year 2010
Where BIBE
Authors Haiyun Lu, Shamima Banu Bte Sm Rashid, Hao Li, Wee Kheng Leow, Yih-Cherng Liou
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