News

News articles published in March

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Our recent focus on Covid19, Coronavirus research together with outreach from our community and partners like: Nvidia, PCMR, Github, Razer, Intel, Ubisoft and more. Has led to some interest from…

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Investigating Cryptic Binding Sites by Molecular Dynamics Simulations.

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ConspectusThis Account highlights recent advances and discusses major challenges in investigations of cryptic (hidden) binding sites by molecular simulations. Cryptic binding sites are not visible in protein targets crystallized without a ligand and only become visible crystallographically upon binding events. These sites have been shown to be druggable and might provide a rare opportunity to target difficult proteins. However, due to their hidden nature, they are difficult to find thro…

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Microcanonical coarse-graining of the kinetic Ising model.

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We propose a scheme for coarse-graining the dynamics of the 2-D kinetic Ising model onto the microcanonical ensemble. At subcritical temperatures, 2-D and higher-dimensional Ising lattices possess two basins of attraction separated by a free energy barrier. Projecting onto the microcanonical ensemble has the advantage that the dependence of the crossing rate constant on environmental conditions can be obtained from a single Monte Carlo trajectory. Using various numerical methods, we com…

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Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge.

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The SAMPL Challenges aim to focus the biomolecular and physical modeling community on issues that limit the accuracy of predictive modeling of protein-ligand binding for rational drug design. In the SAMPL5 log D Challenge, designed to benchmark the accuracy of methods for predicting drug-like small molecule transfer free energies from aqueous to nonpolar phases, participants found it difficult to make accurate predictions due to the complexity of protonation state issues. In the SA…

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