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Examples are presented illustrating the close proximity of some indels to established small-molecule binding pockets that can potentially facilitate selective targeting to the parasites and bypassing their host, thus reducing or eliminating the toxicity of the potential drugs.
Structural data show that these compounds make unique contacts with several amino acids in the enzymes hydrophilic and hydrophobic binding pockets that can be exploited for design of isoform specific CAIs [ 127].
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TIR1 contains a binding pocket that can bind IAA and can also bind two auxin analogs, 2,4-D and 1-napthalenacetic acid (1-NAA) [10], [15], [63].
Mutational and computational analysis of A1-AR revealed a distinct conformation of the second extracellular loop and a wider extracellular cavity with a secondary binding pocket that can accommodate orthosteric and allosteric ligands.
Recent successes in identifying potent NNIs are reviewed with an emphasis on the recent trend of utilizing a computer model of HIV RT to identify space in the NNI binding pocket that can be exploited by carefully chosen functional groups predicted to interact favorably with binding pocket residues.
The mSAA3 tetramer forms a hollow hydrophobic binding pocket that can accommodate retinol.
The PAZ domain contains a specific binding pocket that can anchor sRNA duplexes with two-nucleotide 3′ overhang.
Finally, we provide structural insight into the binding interaction by solving the mouse SAA3 crystal structure, which reveals a tetrameric assembly with a hydrophobic binding pocket that can accommodate retinol.
We determined the crystal structure of mouse SAA3 at a resolution of 2 Å, finding that it forms a tetramer with a hydrophobic binding pocket that can accommodate retinol.
A distinction between pol η and other Y-family DNA polymerases is that the polymerase core is rotated away from the little finger domain to create even a larger binding pocket that can accommodate two nucleotides (as in the case of pyrimidine pyrimidine dimer) into the pol η binding site.
This structure makes the DNA-binding pocket that can accommodate homologous pairing between the invading strand and the complimentary strand in the template DNA [ 76].
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