Here is an updated list of affordable (APC < $2000) impact neutral and other select OA publishing options for chemistry Impact neutral journals \$1195 PeerJ Chemistry journals. Open peer review. (Disclaimer I am Editor-in-chief for PeerJ Physical Chemistry). PeerJ also has a membership model, which may be cheaper than the APC. \$1210 Results in Chemistry. Closed peer review \$1350 F1000Research. Open peer review. Bio-related \$1595 PeerJ - Life and Environment. Open peer review. Bio-related. PeerJ also has a membership model, which may ..read more

    Here is an updated list of affordable impact neutral and other select OA publishing options for chemistry Impact neutral journals \$1000 Results in Chemistry. Closed peer review \$1195 PeerJ Chemistry journals. Open peer review. (Disclaimer I am an editor for PeerJ Physical Chemistry). PeerJ also has a membership model, which may be cheaper than the APC. \$1195 PeerJ - Life and Environment. Open peer review. Bio-related. PeerJ also has a membership model, which may be cheaper than the APC. \$1250 ACS Omega. Closed peer review.  \$1350  ..read more

I recently developed a ML model to predict pIC50 values for molecules and used it together with a genetic algorithm code to search for molecules with large pIC50 values. However, the GA searches never found molecules with pIC50 values that where larger than in my training set.  This brought up the general question of whether ML models are capable of outputting values that are larger than those found in the training set. I made a simple example to investigate this issue for different ML models. $\mathbf{X}_1 = (1, 0, 0)$ corresponds to 1, $\mathbf{X}_2 = (0, 1, 0)$ corresponds to 2, and ..read more

  Here is an updated list of affordable impact neutral and other select OA publishing options for chemistry Impact neutral journals \$1000 Results in Chemistry. Closed peer review \$1195 PeerJ Chemistry journals. Open peer review. (Disclaimer I am an editor for PeerJ Physical Chemistry). PeerJ also has a membership model, which may be cheaper than the APC. \$1195 PeerJ - Life and Environment. Open peer review. Bio-related. PeerJ also has a membership model, which may be cheaper than the APC. \$1250 ACS Omega. Closed peer review.  \$1350 F1000 ..read more

With RDKit version 2020.09 the drawing code got a major overhaul and, IMO, it can now be used to make figures for publications. Based on Greg Landrum's show_mol function I made a simpler version for multiple molecules that'll also give you png and, especially, pdf files. Blogger doesn't allow you to upload pdf files, so the picture above really doesn't do the corresponding pdf file justice. This work is licensed under a Creative Commons Attribution 4.0 ..read more

  Reaction SMARTS is an RDKit feature that is very useful for generating reactant products pairs for a given reaction. Unfortunately the algorithm changes the atom order between reactants and products, which creates problems one tries to locate the reaction paths using an interpolation-based algorithm such as nudged elastic band (NEB). Fortunately, RDKit keeps track of the the change in atom order (thanks to my MS student Julius Seumer for the tip!) and it's easy to reorder the atoms: def reorder_product(product): reorder_inverse = [int(atom.GetProp('react_atom_idx')) for atom in produ ..read more

  It's almost 3 years ago that I wrote about atom mapper and now the code has received a major overhaul thanks to my PhD student Mads Koerstz. The 2D atom mapping part is basically left untouched, but the main new thing is a general implementation of the 3D mapping problem.  The 3D mapping problem is that if labels (i.e. atom orders) are considered then all tetrahedral centers are chiral and the chirality of centers with equivalent atoms, such as CH2 groups, generated by RDKit's embed function will be arbitrary and unlikely to match in reactants and products. This creates problems fo ..read more

During a Twitter discussion Noel O'Boyle introduced me to Graph Edit Distance (GDE) as a useful measure of molecular similarity. The advantages over other approaches such as Tanimoto similarity is discussed in these slides by Roger Sayle. It turns out Networkx can compute this, so it's relatively easy to interface with RDKit and the implementation is shown below. Unfortunately, the time required for computing GDE increases exponentially with molecule size, so this implementation is not really of practical use. Sayle's slides discusses one solution to this, but it's far from trivial to imple ..read more

Here is an updated list of affordable impact neutral and other select OA publishing options for chemistry Impact neutral journals $0 (in 2020) PeerJ chemistry journals. Open peer review. (Disclaimer I am an editor on PeerJ Physical Chemistry) $638 (normally $850) Results in Chemistry. Closed peer review $750 ACS Omega (+ ACS membership $166/year). Closed peer review. WARNING: not real OA. You still sign away your copyright to the ACS. $1000 F1000Research. Open peer review. Bio-related $1095 PeerJ - Life and Environment. Open peer review. Bio-related. PeerJ also has a membership model ..read more

The Faculty of Science maintains a list of research presentations that high school classes can choose from when planning a visit. The description of the talk can include links to material the students and use to prepare and keep working on after the visit. So I made a series of video lectures about machine learning and Python for people with no other background than high school level mathematics. I hope to add more videos/topics as I find the time and I hope this will get some of the students interested in programming and machine learning. This work is licensed under a Creative Commons ..read more