The phrase "accommodate the side" is correct and usable in written English.
It can be used in contexts where you are discussing making adjustments or provisions for a particular aspect or group.
Example: "In order to ensure a smooth collaboration, we need to accommodate the side that has specific requirements."
Alternatives: "make room for the side" or "adjust for the side".
Class II molecules have polymorphic pockets that accommodate the side chains of bound peptides.
RosettaDock uses a low resolution Monte Carlo search and backbone optimization algorithm to optimally position a submitted monomer pair, followed by a refinement to relax the backbone and accommodate the side chains (Gray et al. 2003).
RosettaDock is a server that uses a low-resolution Monte Carlo search and backbone optimization algorithm to position the submitted chain pair, followed by a refinement to relax the backbone and accommodate the side chains (Gray et al. 2003).
We do not observe a direct effect of the side chain volume on the nitrite reduction rates as we see in Phe28 or His64; it is possible that significant rearrangements in the heme pocket are required to accommodate the side chain changes.
Further, the binding site can co-opt the same or similar pockets (hydrophobic, pockets 2 and 3) to accommodate the side chains, linking their formation and dissolution with the different states in the transport cycle to facilitate peptide recognition and release (Fig 4).
We find that some shallow pockets near the known active pocket are very important which can accommodate the side-chains of the inhibitor.
The pocket accommodating the side chain of Tyr18 is mainly composed of several hydrophobic residues including Ile23, Lys51 and Leu53 of LC3B, and forms a hydrogen bond between the carbonyl oxygen of LC3B and19 and the hydroxyl group of FUNDC1 Tyr18 (Fig. 3A).
This subsite accommodates the side chain of BR22, which forms a direct hydrogen bond with the hydroxyl group of TY60A.
In the ligand-complex the pocket accommodates the side chain of a key anchor residue of the peptide (Fig. 1A).
The amino acid side chain of a mutant at this position would point into a hydrophobic niche that also accommodates the side chain of L574 from another monomer.
It is located within the peptide binding site and accommodates the side chain of a key-anchor residue of the peptide ligand.
