Version 2.3 (March 2014)
Jmol was upgraded to the latest version (Jmol-14.0.11). This version is compatible with the most updated security requirements of Java.
Version 2.2 (March 2013)
What is new in version 2.2?
Please note that due to the changes described above, there may be certain discrepancies between the patch calculated using version 2.2 and the patch calculated using the previous version.
The electrostatic potential calculation is now conducted by the APBS software.
The grid size is now dynamically set for each protein chain and there is no limitation of the protein chain size.
The Patch Finder algorithm was improved in terms of accuracy and efficiency.
Version 2.1 (May 2012)
The selection of a chain identifier is now optional. By default, all protein chains are calculated (each chain is calculated separately).
In case the calculation is performed on more than one chain, the largest positive patch of the first protein chain is initially displayed in the results page.
The display can be change to each of the other protein chains.
Version 2.0 (Oct. 2011)
What is new in version 2.0?
The assignment of hydrogen atoms to the protein structure is conducted by the program PDB2PQR instead of HBPLUS.
In order to allow more accurate electrostatic potential calculation of large proteins, several parameters
used by UHBD have been changed:
- Default grid dimensions were changed to 85x85x85. For larger protein chains the dimensions are automatically increased to 110x110x110.
- Grid spacing was changed to 1Å.
Shula Shazman, Gershon Celniker, Omer Haber, Fabian Glaser, Yael Mandel-Gutfreund (2007) Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces. Nucleic Acids Res., 35:526-30.