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This was done for all HLA molecules represented in the data set.
The second level is a set of molecular binding prediction methods that are used to compute the binding affinity of the molecules represented in the agent-based model.
These paths are then reduced to directed interactions between signaling molecules represented in a SIF.
As of September 24 , 2012 there are 12,785 chemically distinct ligand molecules represented in at least one PDB structure.
The output of PERA is a set of directed interactions between signaling molecules represented in a Simple Interaction Format (SIF).
Using an estimation of the C. gigas genome size of about 823 Mb, the number of molecules represented in 20 ng of gDNA was then calculated.
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The distance unit is given by the radius of the smallest molecule represented in the model and corresponds to 0.323 × 10−3 μm.
Proteins, ligands and parameters are stored in molecules (represented by class molecule_t), and are composed of MOs (atom, residue, etc).. Molecules are stored in database (represented by class database_t).
The persistence and evolution of all life forms on earth is ensured by replication of nucleic acid molecules (represented by double-stranded DNA in all extant cellular organisms but by single-stranded DNA or RNA in numerous viruses).
As evidence that the increase in matrix molecules represented de novo fibrogenesis, we also stained for alpha-smooth muscle actin (α-SMA), which is a marker of activated hepatic stellate cells [ 23].
Clusters #5, #20 and #21 could be methodological "artifacts" arising from the way molecules are represented in KEGG and the way we translate them into atom triplets.
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