Nvidia ends support for 32bit
Nvidia has ceased to support 32bit platform. You can read more here. If you’re running a 32-bit version of Windows 7, Windows 8, Windows 10, or any flavour of Linux,…
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AI for Drug Discovery in Two Stories
TL;DR: Today, we are excited to share two papers that tell distinct stories about AI drug discovery: 1. “Spatial Graph Convolutions for Drug Discovery” describes new deep neural network architectures…
Read moreQuantitative self-assembly prediction yields targeted nanomedicines.
Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of s…
Read moreTransferable neural networks for enhanced sampling of protein dynamics.
Transferable neural networks for enhanced sampling of protein dynamics. J Chem Theory Comput. 2018 Mar 12;: Authors: Sultan MM, Wayment-Steele HK, Pande VS Abstract Variational auto-encoder frameworks have demonstrated success…
Read moreElectron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly.
Ebola virus nucleoprotein (eNP) assembles into higher-ordered structures that form the viral nucleocapsid (NC) and serve as the scaffold for viral RNA synthesis. However, molecular insights into the NCÂ assembly process are lacking. Using a hybrid approach, we characterized the NC-like assembly of eNP, identified novel regulatory elements, and described how these elements impact function. We generated a three-dimensional structure of the eNP NC-like assembly at 5.8Â Ă… using electron cryo-microsc…
Read moreA dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation.
Many eukaryotic protein kinases are activated by phosphorylation on a specific conserved residue in the regulatory activation loop, a post-translational modification thought to stabilize the active DFG-In state of the catalytic domain. Here we use a battery of spectroscopic methods that track different catalytic elements of the kinase domain to show that the ~100 fold activation of the mitotic kinase Aurora A (AurA) by phosphorylation occurs without a population shift from the DFG-Out to the D…
Read moreTheoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics.
Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics. J Chem Phys. 2018 Jan 28;148(4):044111 Authors: Sinitskiy AV, Pande VS Abstract Markov state models (MSMs)…
Read moreREDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment.
REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment. ACS Cent Sci. 2018 Jan 24;4(1):89-96 Authors: Yang H, Staveness D, Ryckbosch SM, Axtman AD,…
Read moreAndroid client overhaul
  “In October 2017 we announced the open sourcing of the Folding@Home Android client developed by Sony.  We want to thank everyone who have contributed with CPU time. From the 16th…
Read moreWarfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer.
Although warfarin is the most widely used anticoagulant worldwide, the mechanism by which warfarin inhibits its target, human vitamin K epoxide reductase (hVKOR), remains unclear. Here we show that warfarin blocks a dynamic electron-transfer process in hVKOR. A major fraction of cellular hVKOR is in an intermediate redox state containing a Cys51-Cys132 disulfide, a characteristic accommodated by a four-transmembrane-helix structure of hVKOR. Warfarin selectively inhibits this major cellular fo…
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