The company failed to see that sinking the Spar would set a precedent for dealing with other obsolete structures in the North Sea and that it was probably the worst structure to start with given its size and toxic residues.
Next, we purified the mutant variant of PKD1 predicted to perturb the determinant of specificity in alignment position 494 that we named αD1, given its location on the first residue of α helix D of the kinase domain.
Similarly, for a given residue, its local three-state secondary structure profile was taken from a sliding window of 15 consecutive residues.
For a given residue, its local sequence fragment was extracted and encoded as a 20×(2l+1 -dimensional vector using a sliding window scheme, where l denotes the half window size and 2l+1 -dimensionalwindow length.
Identification of ATP-binding sites can be addressed as a two-classification problem, i.e., determining whether a given residue is binding residue or not.
The B-factor is a measure of the average deviation of a given residue from its mean position in the crystal structure.
Given a residue, we consider its directly broken interfacial atomic contacts, namely those contacts formed by an atom other than C, N, O, C α or C (these atoms are the remainder after a residue is mutated into alanine) and any contact partner from the other chain, even its backbone atoms.
Figure 1a shows the total correlation, CT, of a given residue, presented as the residue index along the abscissa, obtained by using 1NI6.pdb.
For a given residue on the surface, its neighbors are the residues on the surface with distance to the given residue <10 angstroms.
The neighboring residues of a given residue play an important role in shaping the mutation pattern of the residue.
As a consequence, it could not be assumed that adduct formation at a given cysteine residue had toxicological relevance.
