Category Archives: Cheminformatics

A tougher molecular data split – spectral split

Scaffold splits have been widely used in molecular machine learning which involves identifying chemical scaffolds in the data set and ensuring scaffolds present in the train and test sets do not overlap. However, two very similar molecules can have differing scaffolds. In an example provided by Pat Walters in his article on splitting chemical data last month, he provides an example where two molecules just differ by a single atom and thus have a very high Tanimoto similarity score of 0.66. However, they have different scaffolds (figure below).

In this case, if one of the molecules were in the train set and the other in the test set, predicting the test molecule would be quite trivial as there is data leakage. Therefore, we need a better splitting method such that there is minimal overlap between the train and test set. In this blogpost, I will be discussing spectral split, a splitting method introduced by our fellow OPIG member, Klarner et. al (2023).

Spectral split

Spectral split or clustering is based on the spectral graph partitioning algorithm. The basic idea of spectral clustering is as follows: The dataset is projected on a R^n matrix. An affinity matrix using a kernel that could be domain-specific is defined. Following that, the graph Laplacian is computed from the affinity matrix, followed by its eigendecomposition. Then,  k eigenvectors corresponding to the k lowest/highest eigenvalues are selected. Finally, the clusters are formed using k-means.

In the context of molecular data splitting, one could use the Tanimoto similarity metric to construct a similarity matrix between all the molecules in the dataset. Then, a spectral clustering method could be used to partition the similarity matrix such that the similarity within the cluster is maximized whereas the similarity between the clusters is minimized. Spectral split showed the least overlap between train (blue) and test (red) set molecules compared to scaffold splits (figure from Klarner at. al. (2024) below)

In addition to spectral splits, one could attempt other tougher splits one could attempt such as UMAP splits suggested by Guo et. al. (2024). For a detailed comparison between UMAP splits and other commonly used splits please refer to Pat Walters’ article on splitting chemical data.

Controlling PyMol from afar

Do you keep downloading .pdb and .sdf files and loading them into PyMol repeatedly?

If yes, then PyMol remote might be just for you. With PyMol remote, you can control a PyMol session running on your laptop from any other machine. For example, from a Jupyter Notebook running on your HPC cluster.

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The XChem trove of protein–small-molecules structures not in the PDB

The XChem facility at Diamond Light Source is truly impressive feat of automation in fragment-based drug discovery, where visitors comes clutching a styrofoam ice box teeming with apo-form protein crystals, which the shifter soaks with compounds from one or more fragment libraries and a robot at the i04-1 beamline kindly processes each of the thousands of crystal-laden pins, while the visitor enjoys the excellent food in the Diamond canteen (R22). I would especially recommend the jambalaya. Following data collection, the magic of data processing happens: the PanDDA method is used to find partial occupancy in the density, which is processed semi-automatedly and most open targets are uploaded in the Fragalysis web app allowing the ligand binding to be studied and further compounds elaborated. This collection of targets bound to hundreds of small molecules is a true treasure trove of data as many have yet to be deposited in the PDB, making it a perfect test set for algorithm design: fragments are notorious fickle to model and deep learning models cannot cheat by remembering these from the protein database.

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Out of the box RDKit-valid is an imperfect metric: a review of the KekulizeException and nitrogen protonation to correct this

In deep learning based compound generation models the metric of fraction of RDKit-valid compounds is ubiquitous, but is problematic from the cheminformatics viewpoint as a large fraction may be driven by pyrrolic nitrogens (see below) rather than Texas carbons (carbon with 5 bonds like the Star of Texas). In RDKit, no error is more irksome that the KekulizeException or ValenceException from RDKit sanitisation. These are raised when the molecule is not correct. This would make the RDKit-valid a good metric, except for a small detail: the validity is as interpreted from the the stated implicit and explicit hydrogens and formal charges on the atoms, which most models do not assign. Therefore, a compound may not be RDKit-valid because it is actually impossible, like a Texas carbon, but in many cases it is because the formal charge or implicit hydrogen numbers of some atoms are incorrect. In both case, the major culprit is nitrogen. Herein I go through what they are and how to fix them, with a focus on aromatic nitrogens.

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I really hope my compounds get the green light

As a cheminformatician in a drug discovery campaign or an algorithm developer making the perfect Figure 1, when one generates a list of compounds for a given target there is a deep desire that the compounds are well received by the reviewer, be it a med chemist on the team or a peer reviewer. This is despite scientific rigour and training and is due to the time invested. So to avoid the slightest shadow of med chem grey zone, here is a hopefully handy filter against common medchem grey-zone groups.

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Making your code pip installable

aka when to use a CutomBuildCommand or a CustomInstallCommand when building python packages with setup.py

Bioinformatics software is complicated, and often a little bit messy. Recently I found myself wading through a python package building quagmire and thought I could share something I learnt about when to use a custom build command and when to use a custom install command. I have also provided some information about how to copy executables to your package installation bin. **ChatGPT wrote the initial skeleton draft of this post, and I have corrected and edited.

Next time you need to create a pip installable package yourself, hopefully this can save you some time!

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Sort and Slice Tutorial – An alternative to extended connectivity fingerprints

Incorporating conformer ensembles for better molecular representation learning

Conformer ensemble of tryptophan from Seibert et. al.

The spatial or 3D structure of a molecule is particularly relevant to modeling its activity in QSAR. The 3D structural information affects molecular properties and chemical reactivities and thus it is important to incorporate them in deep learning models built for molecules. A key aspect of the spatial structure of molecules is the flexible distribution of their constituent atoms known as conformation. Given the temperature of a molecular system, the probability of each of its possible conformation is defined by its formation energy and this follows a Boltzmann distribution [McQuarrie and Simon, 1997]. The Boltzmann distribution tells us the probability of a certain confirmation given its potential energy. The different conformations of a molecule could result in different properties and activity. Therefore, it is imperative to consider multiple conformers in molecular deep learning to ensure that the notion of conformational flexibility is embedded in the model developed. The model should also be able to capture the Boltzmann distribution of the potential energy related to the conformers.

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Comparing pose and affinity prediction methods for follow-up designs from fragments

In any task in the realm of virtual screening, there need to be many filters applied to a dataset of ligands to downselect the ‘best’ ones on a number of parameters to produce a manageable size. One popular filter is if a compound has a physical pose and good affinity as predicted by tools such as docking or energy minimisation. In my pipeline for downselecting elaborations of compounds proposed as fragment follow-ups, I calculate the pose and ΔΔG by energy minimizing the ligand with atom restraints to matching atoms in the fragment inspiration. I either use RDKit using its MMFF94 forcefield or PyRosetta using its ref2015 scorefunction, all made possible by the lovely tool Fragmenstein.

With RDKit as the minimizer the protein neighborhood around the ligand is fixed and placements take on average 21s whereas with PyRosetta placements, they take on average 238s (and I can run placements in parallel luckily). I would ideally like to use RDKit as the placement method since it is so fast and I would like to perform 500K within a few days but, I wanted to confirm that RDKit is ‘good enough’ compared to the slightly more rigorous tool PyRosetta (it allows residues to relax and samples more conformations with the longer runtime I think).

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Fine-tune generated molecular poses with a force field

Some molecular pose generation methods benefit from an energy relaxation post-processing step.

Predicted pose before energy minimization
Example of a small molecule pose before and after energy minimization. The pose before minimization is shown in white, the optimized prediction is shown in pink, and a crystal pose is shown as reference in light blue. Note how the aromatic rings are flattened and the leftmost bond is shortened by the optimization.

Here is a quick way to do this using OpenMM via a short script I prepared:

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