SDA
Simulation
of Diffusional Association including metal docking code
(version
6)
SDA examples are included in the distribution. You can online browse through them here. The following table gives information about what the respective example demonstrates:
| Solute 1 | Solute 2 | Procedure/Methodology/Features | Calculation type | Example name and link |
|---|---|---|---|---|
| Barnase | Barstar | Bimolecular associaton rate calculation | Tutorial (located in the examples/tutorial/ directory in the downloaded version) | tutorial |
| Barnase | Barstar | UHBD | Bimolecular Association Rate Constant | bnbs |
| Barnase | Barstar | APBS | Bimolecular Association Rate Constant | bnbs-apbs |
| Barnase | Barstar | UHBD | Docking Complexes | bnbs-docking |
| Neutral Gold Surface | Barstar | UHBD based on pqr file for barstar | Docking Complexes | aubs |
| Neutral Gold Surface | Barstar | UHBD based on pqr file for barstar | PMF and Adsoption free energy calculation of docked complexes | aubs-pmf |
| Neutral Gold Surface | Barstar | UHBD based on pqr file for barstar | Docking Complexes | aubs-pqr |
| cytochrome f | plastocyanin | UHBD | Calculation of electron transfer rates | cytf-pc-et |
$LastChangedDate: 2010-10-08 12:37:52 +0200 (Fri, 08 Oct 2010) $ by $Author: richtesn $