Citation: Tao Lu, Yuan Yuan Qiao, Pan Wen Shen. Molecular path for ligand search[J]. Chinese Chemical Letters, ;2011, 22(9): 1130-1134. doi: 10.1016/j.cclet.2011.05.001 shu

Molecular path for ligand search

College of Chemistry, Nankai University, Tianjin 300071, China

Received Date: 28 February 2011

A ligand is a small molecule bind to several residues of a receptor. We adapt the concept of molecular path for effective ligand search with its contacting residues. Additionally, we allow wild type definitions on atoms and bonds of molecular paths for fuzzy algorithms on structural match. We choose hydrogen bond interactions to characterize the binding mode of a ligand by several proper molecular paths and use them to query the deposited ligands in PDBe that interact with their residues in the same way. Expression of molecular path and format of database entries are described with examples. Our molecular path provides a new approach to explore the ligand-receptor interactions and to provide structural framework reference on new ligand design.
- Ligand,
- Residue,
- Path,
- Database
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