Anchor prediction
Hierarchical clustering (Kozakov, Clodfelter, Vajda & Camacho, 2005)
determined the most stable conformation of dipeptides between
A1 and L5. Clustering is based on the
Root Mean Square Deviation (RMSD) between MDS snapshots less than 1 Å
for A1R2,
R2S3,
S3R4, and
R4L5. We also determined the contacts of
side chains as a proxy for ability to bind the receptor, i.e., if side
chains are interacting with each other, their interaction with the
receptor is hindered. Atomic contacts are defined as atoms from the
peptide that are less than 3.8 Å of Cβ-alanine, [Nε, NH2]-arginine,
Cβ-serine, [Cδ1, Cδ2]-leucine from dipeptides. The prediction is
that the stable motif accessible to solvent is critical for molecular
recognition, i.e., the anchor of the protein-protein interaction
(Rajamani, Thiel, Vajda & Camacho, 2004).