Sentence examples for residue environment from inspiring English sources
Although there are limited experimental data, we found statistically significant changes in rotamer preferences depending on the residue environment.
Indeed, coevolution is difficult to detect due to the variable nature of compensatory mutations, the strong dependence of covariations on evolutionary distances, number of sequences in the alignment and residue environment.
mCSM considers only the residue environment in the wild-type protein.
This membrane environment-specific energy function includes residue environment, residue residue interactions and residue density terms.
In this way, mCSM perceives residue environment density and depth implicitly, without relying on direct calculations or thresholds.
The weighted-contact number model (WCN) [ 15, 16] is used to calculate structural flexibility of residue environment.
The approach, called mutation Cutoff Scanning Matrix (henceforth called mCSM), encodes distance patterns between atoms to represent protein residue environments.
An alternative approach to study mutations is to represent residue environments as graphs where nodes are the atoms and the edges are the physicochemical interactions established among them.
Figure 1b summarizes the mCSM prediction workflow as follows: preprocessing the thermodynamic and structural data, extracting the residue environments, signature calculation and noise reduction, supervised learning and mutation impact prediction and validation.
For example, in order to create an automated annotation process involving the appropriate knowledge representation and prediction of functionally important residue environments, a method for extraction of features from sequence, sequence alignments, three-dimensional structure, and structural environment conservation in catalytic sites was recently proposed [ 85].
The fluorescence spectrum of this intermediate was slightly red-shifted, suggesting that the Trp residues environments were not appreciably altered.
