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Moreover, it is anticipated that the proposed method could be extended to other graphical representations of protein sequence and be helpful in future research.
Liu et al. [18] collected a set of figures and classified them according to whether or not they depicted schematic representations of protein interactions.
Here, we consider residue interaction graphs (RIGs) as network representations of protein structures with residues as nodes and inter-residue interactions as edges.
From the above analyses, we conclude that GEO-3D graphs are the best-fitting null model for various graph representations of protein structures.
Parametric representations of protein molecular surfaces are a compact way to describe a surface, and are useful for the evaluation of surface properties such as the normal vector, principal curvatures, and principal curvature directions [22].
Recently, many graphical representations of protein sequences are generated according to the physicochemical properties of 20 AAs [ 15– 215.
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Simple and concise representations of protein-folding patterns provide powerful abstractions for visualizations, comparisons, classifications, searching and aligning structural data.
Although the Gaussian components do not exactly represent the spectra of pure compounds, the results strongly suggest that these fitted components are convenient representations of protein-bound and free NADH.
2D Representations of protein-ligand complexes from modeled structures were created using LigPlot (Cambridge, UK), the output of which was then augmented by 2D representations of substrates generated by MARVINVIEW® (ChemAxon, Budapest, Hungary) to distinguish between the steric orientation of 7α- and 7βOHC.
28 PyMOL was used to obtain graphical representations of proteins in the Protein Data Bank and the amino acid residues are in contact with the ligand.
As educators, we tend to rely largely on readily available static and highly schematized representations of proteins outside their cellular context representations that lack critical structural and kinetic information and convey misconceptions about the nature of the molecular world.
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