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The process and design parameters were optimized to reduce the Net Specific Energy Consumption (NSEC) of the system.
The templated structure was then subjected to 50 nsec of dynamics without constraints to refine the structure.
After pre-run solvent equilibration the peptides were subjected to 100 nsec of free MD simulations at 300°K without any experimental constraints, utilizing Berendsen temperature and pressure coupling and the Particle Mesh Ewald method for evaluating long-range electrostatic interactions.
In silico analysis of the ATP-bound motor domain simulations showed that deviation of all backbone atoms in the motor domain complex in comparison to the crystal structure was small for both mutant and polymorphic variants compared to WT, with an overall root mean square deviation (RMSD) ranging from 1.2 to 2.7 Å, plateauing after 2 nsec of simulation at 2.4 Å RMSD from the starting structure.
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Because PASTA and AGGRESCAN programs both predict that the S-MB sequence containing residues Tyr-7 to Arg-12 is the most stable β-sheet pairing, initial ZDOCK searches were performed with a 49.8 nsec simulation of the MD run of monomer S-MB in 40% HFIP/60% water.
The environment for the resulting "0 nsec" structure of dimer S-MB thus closely approximates that of our SDS-PAGE experiments, which similarly use a loading buffer containing submicellar SDS at a detergent/peptide molar ratio of ∼28/1 (Fig. 8).
To calculate the SNR we used the maximum (absolute) amplitude among the multipath components, and normalized its square by the noise variance, calculated from a late 5 nsec section of the response over all the available receiver positions.
The final "100 nsec" ensemble of MB, HFIP and water molecules also demonstrates that the amphipathic MB peptides sequesters HFIP (not shown), comparably to that previously observed for melittin in HFIP/water mixtures [71], [88].
The final (5-nsec) conformation of VLDPKpSKEDDRYLKFR is shown in Figure 5. Interaction of the peptide with the {100} face involves the central acid amino acids (EDD), while the more basic and hydrophobic N- and C-terminal ends do not form attachments with the crystal.
An energy window of 350 750 keV, a coincidence timing window of 6 nsec, and an acquisition time of 10 20 min. were used.
Each existing NSEC-record, of whom as many exist as names exist for a domain, is ultimately signed by an RRSIG-record to confirm authenticity of the claimed non-existence.
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