Macs in Chemistry

Insanely Great Science

The SAMPL6 Blind Prediction Challenge for Computational Chemistry

 

SAMPL6 includes challenges based on aqueous host-guest binding data (binding free energies and, optionally, binding enthalpies) for three different host molecules; and on physical properties (distribution coefficients and possibly solubilities), for a set of fragment-like molecules. The host-guest systems are useful to test simulation methods, force fields, and solvent models, in the context of binding, without posing the setup issues and computational burden of protein simulations. The physical properties offer efficient tests of force field accuracy when detailed simulations are used, and can also test pKa prediction methods, continuum solvation models, and knowledge-based prediction methods. SAMPL6 will also introduce a new challenge component, the “SAMPLing challenge”, in which computational methods will be evaluated on how efficiently their calculations approach well-converged reference results generated by the organizers. Participants will be provided with machine readable setup files for the molecular systems, including force field setups, along with recommended cutoffs and treatments of long-ranged interactions. The SAMPLing challenge is expected to include one or more cases from each challenge component (host-guest binding on each system; log D calculation).

If you would like to participate in the challenge join up here.


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SAMSON, Software for Adaptive Modeling and Simulation Of Nanosystems

 

SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON's generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means "Software for Adaptive Modeling and Simulation Of Nanosystems.

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SAMSON has an open architecture which allows anyone to extend it - and adapt it to their needs - by downloading SAMSON Elements (modules). SAMSON Elements come in many flavors: apps, editors, controllers, models, parsers, etc., and are adapted to different application domains. SAMSON Elements help users build new models, perform calculations, run interactive or offline simulations, visualize and interpret results, and more. Add new SAMSON Elements to SAMSON straight from SAMSON Connect.

In the latest news Python scripting is coming to SAMSON 0.7.0. Most of the SAMSON API is now exposed in Python, and this will allow you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts. Python will make it even easier to integrate and pipeline SAMSON and SAMSON Elements with well-known packages from diverse fields, e.g. TensorFlow, PyRosetta, RDKit, ASE, etc., to name a few


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SeeSAR Updated

 

SeeSAR 7.1 has just been released.

  • 3D-pharmacophores to identify compounds of interest By now, you can run so many bulk actions, your solution list will grow by the minute. This made it just the right time to implement another filter option to help you keep track! Pharmacophore filters can now be defined using so-called sphere constraints. You can apply these pharmacophores at lightning speed to the molecule table and drill down solutions sets quickly and effectively with queries such as: Which molecules have an acceptor at this position? Filter out molecules that occupy this position! Give me all molecules with an aromatic moiety here!
  • Linking and merging fragments with the integrated ReCore It is now possible to enter the 3D molecule editor with more than just one molecule. Among other things, this facilitates linking and merging operations with ReCore. Simply select the atoms you seek to replace (eg the terminal atoms of two fragment binders that should be linked). A click on the ReCore button retrieves for you in seconds fragments that link the two binders, leaving them as closely as possible in place.
  • Better measure and label-options (with adjustable font size) Partially hidden labels in 3D won't bother you anymore! Instead, the simple labels for showing distances, angles, and so on have been upgraded to the more advanced labels which we have always used for Hyde and more recently for displaying torsion information. These labels are movable (simply click and drag) and are always at the front. Plus, as a bonus feature, you may now also adjust the font size on the labels in the appearance settings menu in the toolbar.
  • Parallel high-throughput docking A lot of users have been waiting for this feature! Now bulk docking can be carried out with just one click. Plus we have parallelized the docking calculation so that it now uses all processors on your computer, providing you with solutions swiftly — just as your hardware permits.
  • Multiple selections for bulk actions Frankly speaking we previously "abused" the favorite icon for making selections to initiate bulk actions. This itself undermined the point of being able to mark molecules as favorites. Now you may conveniently select multiple molecules using the new check box feature, and initiate bulk actions on the basis of this selection. For your convenience we also added a few functions to make working with these selections even more effective (un/check all, invert, ...). Just as for the favorites, shift + left mouse click works on the check boxes as a multiple un/check feature.

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BBEdit 12 released

 

BBEdit everyone's favourite text editor has been updated. This looks to be a substantial update with over 100 new features and refinements, the full release notes are available here.

A couple of features look very useful

There's a new submenu on the Edit menu, "Columns". This submenu contains commands to help you work more easily with column-delimited text files. The three basic commands, "Cut Columns", "Copy Columns", and "Clear Columns" work similarly to their top-level analogues. The columns to be cut/copy/cleared are determined by the selection range: to cut a single column, for example, click in the middle of it. You can cut/copy/clear multiple columns by selecting text across them. The "Rearrange Columns" command gives you an easy way to, well, rearrange the columns in a column-delimited text document. Choose the menu command, and then drag the items into the list to order them as you would like, then press the "Apply" button.

There's a new command on the Text menu: "Canonize". This command is useful for doing batch search-and-replace operations in a file, using another file as a list of search-and-replace transformations.

BBEdit 12.0 requires macOS 10.11.6 ("El Capitan") or later, and is compatible with macOS 10.13 "High Sierra". I've added it to the list of Scientific Applications under High Sierra


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iOS 11 overtakes iOS 10

 

According to the data captured by mixpanel three weeks after launch iOS 11 has overtaken iOS 10. This is important information for developers who can start to focus on the latest version of the mobile operating system.

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In contrast for Android there is a much larger spread of operating systems in use.


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