The 3D model can be built based on atomic positions, and colored based on atomic charges, or built based on residue positions, and colored based on residue charges.
Another residue code based scheme, FIR plus two checking modules based on residue code (CRC), was proposed by [29].
The ruler is based on residue positions of chicken sequences.
Moreover, based on the result of the pepscan study of Lajoix et al [37] one residue type, proline is highly inhibitory, in core positions (-4th – 0th) it disrupts binding.
DNA methyltransferase 1 (DNMT1) has been shown to be phosphorylated on multiple serine and threonine residues, based on cell type and physiological conditions.
The Arabidopsis RING proteins were classified into three RING types (RING-H2, RING-HCa, and RING-HCb) and five modified RING types (RING-v, RING-C2, RING-D, RING-S/T, and RING-G) based on the type of Zn-coordinating residues and the number of amino acids between them [ 14].
The inclusion of residue type counts can be physically justified on the basis of a random coil model of the free energy for the isolated peptide, in which each residue makes an additive contribution based on its type.
– the wild type residue and its direct 3D neighbours, based on the wild type 3D model the mutant residue and its direct 3D neighbours, based on the mutant 3D model – residues in contact with the wild type residue and their direct 3D neighbours, based on the wild type 3D model – residues in contact with the mutant residue and their direct 3D neighbours, based on the mutant 3D model.
The new CREDO database now contains the interactions between all surface-exposed residues in biological assemblies and classifies them based on the type of entities involved.
Based on the type of predicted secondary structure element, Henipavirus NTAIL domains may possess two putative α-MoREs (residues 408 422 and 473 493), a putative I-MoRE (residues 523 532) and a putative β-MoRE (residues 444 464).
