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Analysis of the 3D structures of protein ligand binding sites can provide valuable insights for drug discovery.
A structural mapping of protein binding sites can provide a useful tool for probing the three-dimensional structural relationships between biological macromolecules [3, 10].
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Thus, molecular imaging based on small molecule probes with intracellular binding site can provide more roundly information about the c-MET activation status.
Targeting the Abl myristate binding site can provide an important pharmacological tool to suppress the rise of drug resistant mutations, and overcome existent mutations that are resistant to ATP-competitive inhibitors.
These results provide strong biophysical evidence that allosteric interactions play a role in Abl kinase downregulation and that targeting sites outside the ATP binding site can provide an important pharmacological tool to overcome mutations that cause resistance to ATP-competitive inhibitors.
Therefore, each true binding site can provide up to 5 initial solutions that are similar to the real motif.
Since many proteins conduct their molecular functions through the specific recognition of small molecules (ligands), information about the ligand-binding sites can provide insights into their molecular functions (Campbell et al., 2003; Sotriffer and Klebe, 2002).
Since not all cis-elements are known and transcription regulation most likely results from the presence and a combinational use of multiple transcription factor binding sites [21], computational identification of such sites can provide a rapid and cost-effective method for identifying groups of co-expressing genes with high success.
The identification of different ligand binding modes to a secondary site can provide hints for the design of non-ATP-competitive inhibitors targeting the interaction between the α catalytic and the β regulatory subunits.
Comparison of ttGBP and MBP provides a clear example of structural adaptations by which the size of ligand binding sites can be controlled in the PBP super family.
Similarity in ligand binding sites can indicate common binding modes and recognition of similar molecules, allowing potential inference of function for an uncharacterised protein or providing additional evidence of common function where sequence or fold similarity is already known.
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