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The architecture of this model, termed the Homulus DNA model is open (in contrast to the inverted W&C model) and using it might help us to understand the nature of some specific DNA protein interactions, ordered chromatin formation (coiling and de-coiling), specific gene-to-gene interaction (gene targeting).
Similarly, for the DNA model: is the number of paternal assigned reads and is the number of maternal assigned reads.
> In the few cases where a DNA model is selected, it is always a single model covering loop and stem, rather than a model partitioned for stems and loops.
The RNA model is, and the DNA model is, 1 Here the parameterization of the Negative Binomial distribution is such that, if η∼ NegativeBinomial k, ε), then η∈{0,1,… } denotes the number of failures before the first k successes with probability of success equal to ε.
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Then the A-form DNA model was docked into the map and further refined by the Phenix real space protocol to generate the best local fit of model to density.
In 1996, a new technology called the 'sticker DNA' model was introduced by Roweis and colleagues.
The enhancer DNA model was generated using the DNA rebuild module in 3DNA (Lu and Olson, 2003).
A DNA model was generated for all these sequences using the basic step parameter from the NCP-601L nucleosomal crystal structure file (PDB ID: 3UT9) on the 3-D DNA web server.
Other genes involved in B-cell signaling, NF-κB activation, or DNA modeling were found altered, notably TBL1XR1 (33%), MYC (26%) CREBBP (26%), and IRF4 (21%) or HIST1H1E (41%).
The DNA models were enclosed in a cubic box with a volume of 68.47 nm (2.403 nm × 2.901 nm × 4.496 nm) containing TIP3P water molecules as well as Na+ and Cl− counter ions to create a neutral electrostatic environment.
G2PΔN was structurally aligned with RNase H nucleic acid complexes and a B-DNA model was aligned with the nucleic acid from the complex structure (Nowotny et al, 2007).
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