OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput Biol. 2017 Jul 26;13(7):e1005659 Authors: Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA,…
Read moreMolecular simulation has been used to model the detailed folding properties of peptides, yet prospective computational peptide design by such approaches remains challenging and nontrivial. To test the accuracy of simulation-based hairpin design, we characterized the folding properties of a series of so-called β-cap hairpin peptides designed to mimic a conserved hairpin of LapD, a bacterial intracellular signaling protein, both experimentally by NMR spectroscopy and computationally by implicit-…
Read moreIs Multitask Deep Learning Practical for Pharma? J Chem Inf Model. 2017 Jul 10;: Authors: Ramsundar B, Liu B, Wu Z, Verras A, Tudor M, Sheridan RP, Pande VS Abstract…
Read moreThe energy flow during natural photosynthesis is controlled by maintaining the spatial arrangement of pigments, employing helices as scaffolds. In this study, we have developed porphyrin-peptoid (pigment-helix) conjugates (PPCs) that can modulate the donor-acceptor energy transfer efficiency with exceptional precision by controlling the relative distance and orientation of the two pigments. Five donor-acceptor molecular dyads were constructed using zinc porphyrin and free base porphyrin (Zn(i …
Read moreThe Stanford Research Computing Facility hosting some of our key Folding@home servers will be carrying a maintenance to their electricity system on Thursday, July 6th, and Friday, July 7th. We expect most work servers…
Read moreRelated Articles MSMBuilder: Statistical Models for Biomolecular Dynamics. Biophys J. 2017 Jan 10;112(1):10-15 Authors: Harrigan MP, Sultan MM, Hernández CX, Husic BE, Eastman P, Schwantes CR, Beauchamp KA, McGibbon RT,…
Read moreThe oral microbiome is a dynamic environment inhabited by both commensals and pathogens. Among these is Streptococcus mutans, the causative agent of dental caries, the most prevalent childhood disease. Carolacton has remarkably specific activity against S. mutans, causing acid-mediated cell death during biofilm formation; however, its complex structure limits its utility. Herein, we report the diverted total synthesis and biological evaluation of a rationally designed library of simplified ana…
Read moreHello Everyone, SERVERS DOWN JULY 6 & 7,2017 The Stanford Research Computing Facility hosting some of our key Folding@home servers will be carrying a maintenance to their electricity system on Thursday & Friday,…
Read moreThe metabolite 2-hydroxyglutarate (2HG) can be produced as either a D-R- or L-S- enantiomer, each of which inhibits α-ketoglutarate (αKG)-dependent enzymes involved in diverse biologic processes. Oncogenic mutations in isocitrate dehydrogenase (IDH) produce D-2HG, which causes a pathologic blockade in cell differentiation. On the other hand, oxygen limitation leads to accumulation of L-2HG, which can facilitate physiologic adaptation to hypoxic stress in both normal and malignant cells. Here w…
Read moreSolvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review “alchemical” approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a non-physical pathway to compute free energy differe…
Read more