The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures
✍ Scribed by Wang, Renxiao; Fang, Xueliang; Lu, Yipin; Wang, Shaomeng
- Book ID
- 118020001
- Publisher
- American Chemical Society
- Year
- 2004
- Tongue
- English
- Weight
- 62 KB
- Volume
- 47
- Category
- Article
- ISSN
- 0022-2623
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A new simple empirical function has been developed that estimates the free energy of binding for a given protein-ligand complex of known 3D structure. The function takes into account hydrogen bonds, ionic interactions, the lipophilic protein-ligand contact surface and the number of rotatable bonds i
It is shown that the computer program LUDI can be used to search large databases of three-dimensional structures for putative ligands of proteins with known 3D structure. As an example, a subset of =30 000 small molecules (with less than 40 atoms and 0-2 rotatable bonds) from the Fine Chemicals Dire