Macs in Chemistry

Insanely Great Science

Chemistry on Mobile Devices: Create, Compute, Collaborate


Just looking at the speakers at the Mobile Chemistry conference organised by RSC Chemical Information and Computer Applications Group 7 September 2016 10:00-16:30, Cambridge, United Kingdom.

Andy Davies is talking about the RSC Medicinal Chemistry Toolkit app a suite of resources (Chemical Formula, MWt, GCLogP, Ligand Efficiency, Ligand Lipophilic Efficiency and AZFilters calculations) to support the day to day work of a medicinal chemist. Based on the experiences of medicinal chemistry experts, it was developed otherwise difficult-to-access tools in a portable format for use in meetings, on the move and in the lab. The app was developed in collaboration with Molecular Materials Informatics.


The latest version includes computational structural filters developed by AstraZeneca drug design teams. This looks like an excellent opportunity to hear more about this swiss army knife for medicinal chemists and feedback what new features you might want.


SZYBKI v1.9.0 Released


Freeform –calc conf estimates the free energy of transforming a single molecular conformer from an ensemble of solution phase conformers to a single bioactive conformation. Several new features have been added, including:

  • Multiple input conformers can now be tracked. For example, input conformers could be top scoring poses of docked molecules, alternative x-ray conformations (from the PDB), or alternative ligand refinements (e.g. from AFITT).
  • In addition to the standard Sheffield solvation model, Freeform energy calculations can now be run using a Poisson-Boltzmann corrected solvation model.
  • Conformational search has been improved by including solvation throughout the conformational sampling.
  • An extension of the AM1BCC charging model that considers Electrostatically Least-interacting Functional groups (ELF), AM1BCC ELF10, is now the default method for applying partial charges to a ligand. This mitigates electrostatics problems that frequently arise for charged ligands.

  • Support for Mac OS X 10.10 and 10.11 has been added.

  • Mac OS X 10.7 and 10.8 are no longer supported.




Molsoft have just announced and interesting new product ICM-Scarab, a one-stop shop for capturing and analysing bioinformatics and chemoinformatics data. It provides and electronic notebook for storing experimental information integrated with query tools that allow the user to effortlessly search both internal and external SQL databases.

There is a webinar Wed, Jun 29, 2016 5:00 PM - 6:00 PM BST if you want to find out more.


Swift 3


Swift Blog Update

Swift 3 beta was just released as part of Xcode 8 beta and includes numerous enhancements, many contributed by the open source community. The primary goal of Swift 3 is to implement the last major source changes necessary to allow Swift to coalesce as a consistent language throughout, resulting in a much more stable syntax for future releases.


Pymol and very large PDB files. The Zika Cryo-EM structure as a case study


An interesting post on chemistry and computers, Pymol and very large PDB files. The Zika Cryo-EM structure as a case study. Always good to see people stress testing computational tools.