1.0 Blog

This is our blog with all the newest information about webSDA.

30th November 2017

Change in dielectric constant used in Poisson-Boltzmann calculations

We have changed the solute interior dielectric constant used in the Poisson-Boltzmann calculations for generating electrostatic potential grids from 1.0 to 4.0.

9th December 2015

Electrostatic desolvation parameters changed in docking and association simulations

Previously, webSDA used a different model for electrostatic desolvation in docking and association simulations compared to that used in multiple molecule simulations. Docking and association simulations used an ionic strength dependent model for the electrostatic desolvation potential, following the method described in Gabdouline and Wade (2001), J. Mol. Biol., 306, 1139-1155. In multiple molecule simulations an ionic strength independent model was used, as described in Gabdoulline and Wade (2009), J. Am. Chem. Soc., 131, 9230-9238. Now, the latter ionic strength independent term is used in all simulations. If you are comparing new docking or association results to any that you have previously obtained, please be aware of this difference. For information on where you can find more details on the force field used in webSDA, please see the FAQ.

9th December 2015

Soft-core repulsion treatment changed in multiple molecule simulations

The previous treatment of soft-core repulsion used in multiple molecule simulations in webSDA was found to result in overly attractive interactions. Previously, all hydrogen atoms were removed from the structures before the soft-core repulsion grids were generated. This allowed effective charge sites on one solute to penetrate too far into interacting solutes. This has now been altered so that the soft-core repulsion grids are generated with all hydrogen atoms present.

webSDA 1.0 is released!

webSDA is a web interface to run Simulation of Diffusional Association (SDA7)! webSDA supports short SDA simulations and also prepares input files to run on standalone SDA7.

You can write your suggestions for our web server and recommend new features that you want from our web server by clicking "Contact us"! Xiaofeng