HotSprint database can be accessed through a web interface where users can search for computational hot spots in protein interfaces.
The evolutionarily conserved residues are found by Rate4Site algorithm (20). Rate4Site makes use of topology and branch lengths of the phylogenetic trees constructed from multiple sequence alignments (MSA) of proteins and estimates conservation rates of amino acids based on the empirical Bayesian rule. MSAs of proteins constituting interfaces are taken from HSSP (Homology-Derived Secondary Structure of Proteins) (23) database as of 14 January 2006. All MSAs obtained from HSSP are converted to FASTA format to be used in Rate4Site step.
In addition, some residues are more frequently observed to be hot spots, so each of the 20 amino acids has a different propensity to be a hot spot. Hot spot propensities are used to rescale the conservation scores. Further, hot spots prefer to reside in protein cavities (24), therefore surface area accessibility of interface residues are incorporated into our hot spot scoring formula.
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Definition of interface residues
ASA (Solvent-accessible surface area) of a residue was calculated using the program NACCESS. [25] A
residue with an interface area (ΔASA) > 1Å2 is defined as an interface residue and ΔASA is the change in ASA of the
residue upon protein dimer formation from monomer state.
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