Name
Title | ||
|---|---|---|
Pharmacophore Screening of the Protein Data Bank for Specific Binding Site Chemistry. |
Abstract | ||
|---|---|---|
A simple computational approach was developed to screen the Protein Data Bank (PDB) for putative pockets possessing a specific binding site chemistry and geometry. The method employs two commonly used 3D screening technologies, namely identification of cavities in protein structures and pharmacophore screening of chemical libraries. For each protein structure, a pocket finding algorithm is used to extract potential binding sites containing the correct types of residues, which are then stored in a large SDF-formatted virtual library; pharmacophore filters describing the desired binding site chemistry and geometry are then applied to screen this virtual library and identify pockets matching the specified structural chemistry. As an example, this approach was used to screen all human protein structures in the PDB and identify sites having chemistry similar to that of known methyl-lysine binding domains that recognize chromatin methylation marks. The selected genes include known readers of the histone code as well as novel binding pockets that may be involved in epigenetic signaling. Putative allosteric sites were identified on the structures of TP53BP1, L3MBTL3, CHEK1, KDM4A, and CREBBP. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1021/ci900427b | JOURNAL OF CHEMICAL INFORMATION AND MODELING |
Keywords | Field | DocType |
protein data bank,binding site | Pharmacophore,Binding site,Combinatorial chemistry,Chemistry,Bioinformatics,Chromatin,Protein Data Bank,Protein Data Bank (RCSB PDB),Histone code,Protein structure | Journal |
Volume | Issue | ISSN |
50 | 3 | 1549-9596 |
Citations | PageRank | References |
2 | 0.38 | 11 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Valérie Campagna-Slater | 1 | 14 | 2.02 |
| Andrew G Arrowsmith | 2 | 6 | 0.80 |
| Yong Zhao | 3 | 2 | 0.38 |
| Matthieu Schapira | 4 | 21 | 4.41 |