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Riniker lab @ ETHZ @rinikerlab
Joined March 2021
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We're happy to be the #ChemSciPicks of week from @ChemicalScience
Chemical Science@ChemicalScience
19 Jun 2024
This week's #ChemSciPicks comes from Sereina Riniker (@rinikerlab) at ETH Zürich (@ETH_DCHAB) and looks at a general graph neural network based implicit solvation model for organic molecules in water. Read it here: doi.org/10.1039/D4SC02432J
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Our latest preprint introduces and validates a new hybrid classical/ML force field for working with condensed phase systems. It's now up on arXiv: arxiv.org/abs/2308.08984
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We are really happy to announce that @linker_phi's paper on membrane permeability of cyclic peptides has won the @RoySocChem's Outstanding Student Paper award in computational and theoretical chemistry for 2022!
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We're really happy that our most recent publication in @JChemPhys, which introduces a new energy-based clustering algorithm, has been featured by the editors will be the cover image for the next issue. pubs.aip.org/aip/jcp/article…

Energy-based clustering: Fast and robust clustering of data with known likelihood functions

Clustering has become an indispensable tool in the presence of increasingly large and complex datasets. Most clustering algorithms depend, either explicitly or

pubs.aip.org
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The next paper from our collaboration with the @LabZenobi is now out. Here we applied #MolecularDynamics to understand the trends observed in #FRET experiments. pubs.acs.org/doi/10.1021/acs…

Influence of the Fluorophore Mobility on Distance Measurements by Gas-Phase FRET

Gas-phase Förster resonance energy transfer (FRET) combines mass spectrometry and fluorescence spectroscopy for the conformational analysis of mass-selected biomolecular ions. In FRET, fluorophore...

pubs.acs.org
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Our most recent preprint shares an efficient approach for assigning partial charges to atoms in molecules. The method uses a hierarchy created from attention values from a GNN trained on QM data. arxiv.org/abs/2305.15981 It's all #opensource and #opendata, of course.

DASH: Dynamic Attention-Based Substructure Hierarchy for Partial...

We present a robust and computationally efficient approach for assigning partial charges of atoms in molecules. The method is based on a hierarchical tree constructed from attention values...

arxiv.org
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Our second paper that came out today describes @AnnaKamenik's collaboration with the Zenobi group combining experimental and computational techniques to help understand the structures of peptides in the gas phase. nature.com/articles/s41467-0…
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In our most recent publication we use a graph neural network to develop a model for implicit solvation in molecular dynamics simulations of peptides. The code is open source and the model is freely downloadable. pubs.aip.org/aip/jcp/article…

Implicit solvent approach based on generalized Born and transferable graph neural networks for...

Molecular dynamics simulations enable the study of the motion of small and large (bio)molecules and the estimation of their conformational ensembles. The descri

pubs.aip.org
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Interested in water in ligand binding sites? Our newest paper applies RE-EDS to study the thermodynamics of water networks in protein cavities. pubs.acs.org/doi/10.1021/acs…

Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein...

Macromolecular recognition and ligand binding are at the core of biological function and drug discovery efforts. Water molecules play a significant role in mediating the protein–ligand interaction,...

pubs.acs.org
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Our new #preprint introduces SIMPD: an algorithm for creating training/test sets for molecular #machinelearning based on an analysis of a large number of real-world medchem projects. #opensource code and data are in github. chemrxiv.org/engage/chemrxiv…

SIMPD: an Algorithm for Generating Simulated Time Splits for Validating Machine Learning Approaches...

Time-split cross-validation is broadly recognized as the gold standard for validating predictive models intended for use in medicinal chemistry projects. Unfortunately this type of data is not...

chemrxiv.org
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Escape from the curse of dimensionality: Our newest preprint introduces an energy-based clustering algorithm that allows you to avoid common problems with estimated densities. The code is, of course, #opensource arxiv.org/abs/2303.01104 github.com/rinikerlab/Energy…
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We've got a new #preprint up describing an approach for simulating an implicit solvent for MD using transferable graph neural networks. All the code is, of course, #opensource. arxiv.org/abs/2302.09321

Implicit Solvent Approach Based on Generalised Born and...

Molecular dynamics (MD) simulations enable the study of the motion of small and large (bio)molecules and the estimation of their conformational ensembles. The description of the environment...

arxiv.org
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Looking for some insights into the permeation process of your beyond rule-of-five (bRo5) compound? Check out these four permeability steps of a cyclic peptide crossing a lipid membrane: pubs.acs.org/doi/10.1021/acs… #OpenAccess #Compchem #bRo5 #permeability

Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross...

Cyclic peptides extend the druggable target space due to their size, flexibility, and hydrogen-bonding capacity. However, these properties impact also their passive membrane permeability. As the...

pubs.acs.org
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Do you want a small sneak peak? Here is an unbiased MD simulation of a cyclic peptide crossing the membrane
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We are very happy to be starting this multi-year project with our collaborators at @NovartisScience.
D-CHAB@ETH_DCHAB
6 Feb 2023
Congratulations to Sereina Riniker @rinikerlab who is among the recipients of the 2022 NIBR Global Scholars Program @NovartisScience !Each Scholar will receive up to 1 mil USD funding over 3 years along with drug-hunting expertise from #NIBR collaborators. novartis.com/research-develo…
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Our newest paper introduces enu, an #opensource tool for enumerating all isomers (including stereoisomers!) for a given molecular formula. jcheminf.biomedcentral.com/a… You can find the source code for enu on @github: github.com/csms-ethz/CombiFF

Development of an open-source software for isomer enumeration

Journal of Cheminformatics - This article documents enu, a freely-downloadable, open-source and stand-alone program written in C for the enumeration of the constitutional isomers and...

link.springer.com
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Great teamwork and discussions with academic and industry colleagues lead to this perspective looking at machine learning for small-molecule drug discovery. sciencedirect.com/science/ar…
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"Regularized by Physics": our new paper introduces a method for using graph neural networks to parameterize force-field potentials. pubs.acs.org/doi/10.1021/acs…

Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of...

Simulations of molecular systems using electronic structure methods are still not feasible for many systems of biological importance. As a result, empirical methods such as force fields (FF) have...

pubs.acs.org
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Preprint alert. Interested in water molecules that affect ligand binding and affinity to protein pockets? We analyzed their energetic contributions as well as arising solvation correlation effects of water networks. #ComputationalChemistry #DrugDesign chemrxiv.org/engage/chemrxiv…

Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein...

Macromolecular recognition and ligand binding are at the core of biological function and drug discovery efforts. Water molecules play a significant role in mediating the protein-ligand interaction,...

chemrxiv.org
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Hot off the press. We improved our IR spectra alignment algorithm that helps you determining the relative stereochemistry of organic molecules. It compares theoretical and experimental IR spectra of all isomers and finds the best match. Check it out here: pubs.rsc.org/en/content/arti…

Improving the IR spectra alignment algorithm with spectra deconvolution and combination with Raman...

The relative stereochemistry of organic molecules can be determined by comparing theoretical and experimental infrared (IR) spectra of all isomers and assessing the best match. For this purpose, we...

pubs.rsc.org
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