Name
Abstract | ||
|---|---|---|
Conformational searches in molecular docking are a time-consuming process with wide range of applications. Favorable conformations of the ligands that successfully bind with receptors are sought to form stable ligand-receptor complexes. Usually a large number of conformations are generated and their binding energies are examined. We propose adding a geometric screening phase before an energy minimization procedure so that only conformations that geometrically fit in the binding site will be prompted for energy calculation.Geometric screening can drastically reduce the number of conformations to be examined from millions (or higher) to thousands (or lower). The method can also handle cases when there are more variables than geometric constraints. An early-stage implementation is able to finish the geometric filtering of conformations for molecules with up to nine variables in 1 min. To the best of our knowledge, this is the first time such results are reported deterministically.mzhang@mdanderson.org. |
Year | DOI | Venue |
|---|---|---|
2005 | 10.1093/bioinformatics/bti055 | Bioinformatics |
Keywords | Field | DocType |
energy minimization procedure,binding energy,binding site,energy calculation,conformational search,large number,improving conformational search,geometric constraint,geometric screening,early-stage implementation,geometric screening phase,heterodox economics,ecological economics,energy minimization,climate change,molecular docking | Docking (molecular),Binding energy,Computer science,Filter (signal processing),Bioinformatics,Energy minimization,Protein structure | Journal |
Volume | Issue | ISSN |
21 | 5 | 1367-4803 |
Citations | PageRank | References |
7 | 0.73 | 15 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Ming Zhang | 1 | 7 | 1.07 |
| R Allen White | 2 | 7 | 0.73 |
| Liqun Wang | 3 | 7 | 0.73 |
| Ronald Goldman | 4 | 30 | 1.61 |
| Lydia E. Kavraki | 5 | 5370 | 470.50 |
| T. Shaska | 6 | 8 | 1.24 |