Free Energy Perturbation (FEP): Another technique in the drug discovery toolbox
Introduction When I first started using CHARMM over 20 years ago as a PhD student, I regularly came across references ...
A new release of Forge is available today. This minor release brings into the GUI many of the features that you have requested over the last few weeks but also introduces the Forge command line interfaces (for a preview please see this post).
We now support pdb file reading. We see this as particularly useful for proteins that are to be used as excluded volumes in the alignment experiments of Forge because there are many applications for processing proteins that cannot write other file formats. Alongside pdb reading, we’ve added a “Cut” option to the molecular editor that should help process raw pdbs into reference molecules and protein excluded volumes.
Also new in this version is a little checkbox on the process dialogue window that gives you the option to remove existing results before you start the calculation. Combining this with removing processing options when there is no work to be done by these (e.g. all molecules have conformations so the conformation options are disabled) has made the re-processing of molecules using different calculation settings a much smoother process.
There are numerous improvements in the overall functionality of forgeV10 which should make using it an even smoother process, give it a try with a free demo!
They are here! falign, fbuild and fscore together comprise Forge command line. Respectively they align molecules, build 3D QSAR models and score new molecules against existing models or molecules. We’re currently wrapping them into KNIME and pipeline pilot to further enable you to deploy them across your organization with a release expected soon.
For existing users, we’ve kept the falign binary name to improve integration with your custom scripts. All command line options from the old falign are also preserved in the new forge align (falign) so we hope the switch to Forge will be really easy for our existing users. However we’ve also added a host of functionality such as field-guided substructure alignment of molecules so you might want to take a look at all the options and see which to incorporate in your workflows.
You can get a free evaluation of Forge GUI or command lines from our registration page or just drop us an email for a custom solution. Once you’ve got the software then check out our training video and keep an eye on our blog for tips and tricks.