The explanation of "accretion substrate"

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The explanation of "accretion substrate"

Post by lhhai » Mon Nov 07, 2005 7:35 am

Hi all,
When reading the paper: "Fast prediction and visualization of protein binding pockets with PASS.", I encountered the phrase: "accretion substrate" (I quoted the context below). My major is IT, not biology and this term is so confusing for me. Would you mind explaining this term for me ?

Thank in advance

Ly Hoang Hai

"PASS begins by reading the Protein Data Bank (PDB)
coordinates of a target protein and assigning elemental
atomic radii (Table 1). Since a protein with explicitly
represented hydrogen atoms contains less interstitial
volume than one without hydrogen, PASS assigns a
few different parameter values in the two cases. By
default, if less than 20% of the atoms in the protein
PDB file are hydrogen, then all hydrogen atoms
are removed and hydrogen-free parameters are assigned;
otherwise, hydrogen is retained and hydrogeninclusive
parameters are assigned (Table 1). The first
layer of probe spheres is computed by looping over
all unique triplets of protein atoms and, if they are
close enough together, calculating the two locations
at which a probe sphere (of radius Rprobe) may lie
tangential to all three protein atoms (Figure 1; Step
a). Appendix A elucidates this three-point geometry,
which is nontrivial since the radii are not necessarily
equal. To be retained, a putative probe sphere must
survive several filters (Figure 1; Step b). The first condition
is that it cannot overlap with any atoms of the
accretion substrate. The second filter explicitly prohibits
the probe from clashing with any protein atoms,
while the third ensures that the probe be somewhat"

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