TY - JOUR
T1 - AnchorDock
T2 - Blind and flexible anchor-driven peptide docking
AU - Ben-Shimon, Avraham
AU - Niv, Masha Y.
N1 - Publisher Copyright:
© 2015 Elsevier Ltd.
PY - 2015/5/5
Y1 - 2015/5/5
N2 - The huge conformational space stemming from the inherent flexibility of peptides is among the main obstacles to successful and efficient computational modeling of protein-peptide interactions. Current peptide docking methods typically overcome this challenge using prior knowledge from the structure of the complex. Here we introduce AnchorDock, a peptide docking approach, which automatically targets the docking search to the most relevant parts of the conformational space. This is done by precomputing the free peptide's structure and by computationally identifying anchoring spots on the protein surface. Next, a free peptide conformation undergoes anchor-driven simulated annealing molecular dynamics simulations around the predicted anchoring spots. In the challenging task of a completely blind docking test, AnchorDock produced exceptionally good results (backbone root-mean-square deviation ≤ 2.2Å, rank ≤15) for 10 of 13 unbound cases tested. The impressive performance of AnchorDock supports a molecular recognition pathway that is driven via pre-existing local structural elements.
AB - The huge conformational space stemming from the inherent flexibility of peptides is among the main obstacles to successful and efficient computational modeling of protein-peptide interactions. Current peptide docking methods typically overcome this challenge using prior knowledge from the structure of the complex. Here we introduce AnchorDock, a peptide docking approach, which automatically targets the docking search to the most relevant parts of the conformational space. This is done by precomputing the free peptide's structure and by computationally identifying anchoring spots on the protein surface. Next, a free peptide conformation undergoes anchor-driven simulated annealing molecular dynamics simulations around the predicted anchoring spots. In the challenging task of a completely blind docking test, AnchorDock produced exceptionally good results (backbone root-mean-square deviation ≤ 2.2Å, rank ≤15) for 10 of 13 unbound cases tested. The impressive performance of AnchorDock supports a molecular recognition pathway that is driven via pre-existing local structural elements.
UR - http://www.scopus.com/inward/record.url?scp=84930189471&partnerID=8YFLogxK
U2 - 10.1016/j.str.2015.03.010
DO - 10.1016/j.str.2015.03.010
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C2 - 25914054
AN - SCOPUS:84930189471
SN - 0969-2126
VL - 23
SP - 929
EP - 940
JO - Structure
JF - Structure
IS - 5
ER -