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Because all of these structures have more than one ligand that binds to protein, we had a large number of ligand-protein binding structures that could be used for in silico drug screening using chooseLD.
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A de novo drug design methodology was used to generate an initial set of structures that could potentially bind to a putative binding site.
In particular, Salis et al. [ 10] developed the RBS calculator, an algorithm that uses the Nupack suite of RNA folding algorithms [ 119] to calculate free energies of competing RNA structures that could prevent ribosome binding to the RBS.
Company structure: What are company structures that could help in building the Trust currency?
Surprisingly, we also observed that D3 had a unique chemical structure that could be accommodated in the binding pocket of ERα.
SATB1 has the specific MAR binding property and can self-polymerize to establish a birdcage-like structure that could encapsulate the silenced genes [19].
We collected the information about 46659 protein ligand binding sites, that could overlap between structures of one protein.
The structure of survivin does not reveal hydrophobic binding pockets that could serve as docking sites for low molecular-weight ligands.
Leapfrog was able to locate a previously unrecognized binding pocket that could accommodate these otherwise anomalous regions of structure.
For SMAP query structures that were protein complexes containing multiple subunits, if the predicted ligand binding site included residues from distinct subunits, we flagged these as possible ligand binding events that could prevent or disrupt complex formation and therefore function.
Nogales and Wang proposed that the ribbon structure (and the sheet structure in general) could provide a novel surface for microtubule-binding proteins that could recognize surfaces unique to the sheet bond to track microtubule growing ends [5].
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