Macs in Chemistry

Insanely Great Science

Functional Swift Conference 2017 slides available

 

The slides for the Functional Swift Conference 2017 are now online here http://2017.funswiftconf.com.



Comments

ADF Modeling Suite 2017

 

I just got this message

We are proud to announce the 2017 release of the ADF Modeling Suite, with excellent contributions from our collaborators and the continued efforts of the SCM team in Amsterdam.

Exciting new features include
Spectroscopy-

  • Many new NLO properties (TPA, THG, ...): Hu, Autschbach & Jensen
  • Constrained DFT with excited states: Ramos & Pavanello
  • LFDFT for d-d and d-f transitions: Ramanantoanina & Daul
  • CV-DFT for singlet-triplet excitations: Krykunov, Senn, Park & Seidu
  • Faster periodic response with TD(C)DFT, including 2D systems: Raupach
  • VCD analysis tools: Nicu

Reactivity & Analysis-

  • Latest xc functionals (SCAN, MN15-L, ....): interface to libxc 3.0
  • Special points, fat bands and improved pDOS analysis
  • GUI support for NEGF with BAND (Thijssen group, includes self-consistent NEGF, gate & bias potential, spin transport) and post-SCF DFTB-NEGF (Heine group)
  • FDE + local COSMO: Goez & Neugebauer
  • Reactivity descriptors from conceptual DFT and QTAIM: Tognetti & Joubert
  • Geometry optimization with SpinFlip in QUILD: Swart
  • Spin-polarization and l-dependency for DFTB: Melix, Oliveira, Rueger, Heine
  • Much faster periodic DFTB(+D) optimizations, latest DFTB.org parameters freely available
  • eReaxFF including explicit electrons: based on Islam, Verstraelen & van Duin
  • Controllable mass-scaling for force bias Monte Carlo ReaxFF: Bal & Neyts
  • Improved VLE, LLE, IDAC, kOW with reparameterized COSMO-SAC: Chen & Lin

GUI & Builders-

  • Quantum ESPRESSO: GUI interface & binaries
  • MOF builder and UFF4MOFsII: Coupry, Addicoat, Heine
  • Much faster visualization of large and periodic systems
  • Set up and visualize 'molecule gun' calculations with ReaxFF

For a more comprehensive list and details see: www.scm.com/support/release-notes


Comments

Working with MOL2 Structures in DataFrames

 

A great tutorial describing how to use 'Biopandas' MOL2 DataFrames to analyze molecules conveniently.

The Tripos MOL2 format is a common format for working with small molecules.


Comments

Royal Society of Chemistry Twitter Poster Conference

 

The Royal Society of Chemistry Twitter Poster Conference is an online event held entirely over Twitter to bring members of the scientific research community together to share their research, network and engage in scientific debate. Building upon the success of the previous two Analytical Science Twitter Poster Conferences, the 2017 poster conference encompassed all areas of the chemical sciences. The conference reached the scientific research community around the world, achieving 1,650 contributors, 6,473 tweets, an audience of 2,770,749 and 11,841,519 total impressions.


Comments

SeeSAR Updated

 

This new version of SeeSAR an interactive tool for designing/improving ligands for drug discovery. This update comprises another milestone in the evolution of this lightweight 3D modeling package, namely its ability to manage multiple protein structures simultaneously. Oftentimes, you may need to take account of multiple, related protein structures, perhaps either to identify the differences while aiming to achieve specificity, or – just the opposite – to find commonalities, such as when you are trying to ensure all variants of a protein will likely be inhibited. In this first implementation of the multi-protein feature, it is not yet possible to align protein structures but it is necessary to work with pre-aligned structures. Loading multiple proteins

Loading a protein does not now start a new project, but instead the new protein is simply added to a table of loaded proteins. In order to visualize the binding of ligands from the protein file, first select the protein of interest and then select one of the ligands listed in the table. As before, any of these bound ligands can be copied to the molecules table with a click on the molecule icon in the ligand table row. Handling multiple proteins

By default, the proteins chains are colored according to the same coloring scheme as before, with each chain in a different color. In the protein table you may set a unique color for a protein to ease identification that will be used for all components of that protein. If you edit a protein, the edited version of the protein will simply be appended to the table without overwriting the original. It is of course also possible to delete proteins from the table. Finally, you may choose the protein to be used for defining a common binding site from the table, just click the icon to start the binding site definition. Once a common binding site has been defined, a little binding site icon indicates which protein was used. Note that only this particular protein is used for the generation of poses, as well as for optimization and affinity estimation, i.e. the Hyde atom coloring on molecules is shown with respect to this protein.

Viewing multiple proteins

Once a common binding site has been defined on one protein, the binding site itself is shown in greater detail. Now however, the regions of the other proteins in the vicinity of the common binding site are also shown in greater detail. This allows you to see the detail you need when seeking out differences or commonalities but the view may, however, become a little crowded. An enhanced menu under the protein visualization icon allows you to switch on and off different protein components (secondary structure, binding site amino acids, ligands, waters and metals) individually or as a group, and you may also change the visibility of entire proteins at once, all making handling of the view very flexible depending on your needs.

Other improvements

We have fixed some seldom occurring but still irritating issues with the 3D editor and also implemented the possibility to restrict the number of CPUs that SeeSAR may recruit for its computation on the command line. The option --thread-count allows you to limit the number of parallel compute threads as best suited. This feature is particularly useful if you run SeeSAR on a cluster which is controlled by a batch queuing system.

There is a review of an earlier version of SeeSAR here.


Comments