PDBaser 2.0 Patch 1

• Added multiprocessing support, brings huge benefits to batch extraction.
• Fixed an issue where PDBaser would crash if it tries to protonate a chain in a pdb file that isn't of peptidic nature ( exp : oligosaccharides ), PDBaser will now ignore the protonation step of these chains, but will still extract them properly.
• Removed PMW, raises a lot of issues with python 3.10, replaced with a custom tk widget class ( Credits in the file ).
• Added QUIET option to the PDB parser, now only propka and pdb2pqr generate noise ( i'll try to remove that as well )
• removed some unnecessary code and optimized some function calls.

PDBaser 2.0

PDBaser 2.0 🔥

PDBaser is now 1 year old ! To celebrate PDBaser's first anniversary, new features have been implemented !

• New powerful CLI interface added to bring automation and to support batch workloads.
• PDBaser is now able to do titration states prediction and protonation for proteins (Using PROPKA through PDB2PQR).
• Huge performance increases for batch workloads, with multiprocessing support coming in the upcoming patch.

PDBaser 1.9

Optimizations :

• Optimized some functions.
• Updated to python 3.8.5.
• Updated all dependencies.

New Features :

• Added an option to generate and extract binding site from select ligand position ( can vary between 1 and 10 Angstroms ).
• Added an option to keep water molecules when extracting chains.
• Hugely improved UI element placement on Linux, with some minor improvements on Windows.

PDBaser 1.8

New PDBaser updated ❗
Changes :

• Milestone Change : PDBaser is now Compiled with MSVC 14.0 instead of interpreted, Hugely thanks to the Nuitka Compiler, this will provide much quicker opening times and overrall better performance.
• Switched from Openbabel depiction API to pure OASA (You can find it here https://gitlab.com/oasa/oasa, or install it from pip using pip install oasa3).
• Added SVG output support, upscaled PNG output and removed the white default background.
• Setup is now compiled with InnoSetup instead of Advanced installer, VCredist2015 is embedded in the setup, installation is optional.
• Molecular weight of residues is now shown in the depiction.
• New logo.

Fixes :

• Fixed interference issues when PDBaser was installed in a system where open babel 3.1.1 was installed and had BABEL_DIR in environment variables.
• Fixed a huge memory leak when selecting residues.

PDBaser_GUI 1.6

The 1.6 release of PDBaser brings a few new features and some under the hood performance improvement, especially when dealing with very big molecules. new features are :

• Downloading from the PDB directly is now possible.
• Adding hydrogen to outputed residues has been added.
• Added a new progress bar, can be usefull to track progress when downloading a large database from the PDB.
• Names of outputed molecules has been fixed, especially for mol2 files (Fixed name generating as *****).
• Some bug fixes and improvements, mainly UI side.

PDBaser_GUI 1.5

New features added !

• 2D Depiction is here ! With possibility to output the picture as a png image.
• Added compressed PDB files support (.gz, for batch downloads from pdb).
• Improved Extraction performance.

PDBaser_GUI 1.2.1

New 1.2.1 Release :

• Added multiple format output for residues.
• Fixed a bug where PDB proteins were saving twice on each extraction.
• Fixed a bug where overwriting molecules when saving would not work.

PDBaser_GUI

Initial release of the GUI version of PDBaser.
Windows only.
Vcredist C++ 2015 x86 is required.