TY - JOUR
T1 - Taking geometry to its edge
T2 - Fast unbound rigid (and hinge-bent) docking
AU - Schneidman-Duhovny, Dina
AU - Inbar, Yuval
AU - Polak, Vladimir
AU - Shatsky, Maxim
AU - Halperin, Inbal
AU - Benyamini, Hadar
AU - Barzilai, Adi
AU - Dror, Oranit
AU - Haspel, Nurit
AU - Nussinov, Ruth
AU - Wolfson, Haim J.
PY - 2003/7/1
Y1 - 2003/7/1
N2 - We present a very efficient rigid "unbound" soft docking methodology, which is based on detection of geometric shape complementarity, allowing liberal steric clash at the interface. The method is based on local shape feature matching, avoiding the exhaustive search of the 6D transformation space. Our experiments at CAPRI rounds 1 and 2 show that although the method does not perform an exhaustive search of the 6D transformation space, the "correct" solution is never lost. However, such a solution might rank low for large proteins, because there are alternatives with significantly larger geometrically compatible interfaces. In many cases this problem can be resolved by successful a priori focusing on the vicinity of potential binding sites as well as the extension of the technique to flexible (hinge-bent) docking. This is demonstrated in the experiments performed as a lesson from our CAPRI experience.
AB - We present a very efficient rigid "unbound" soft docking methodology, which is based on detection of geometric shape complementarity, allowing liberal steric clash at the interface. The method is based on local shape feature matching, avoiding the exhaustive search of the 6D transformation space. Our experiments at CAPRI rounds 1 and 2 show that although the method does not perform an exhaustive search of the 6D transformation space, the "correct" solution is never lost. However, such a solution might rank low for large proteins, because there are alternatives with significantly larger geometrically compatible interfaces. In many cases this problem can be resolved by successful a priori focusing on the vicinity of potential binding sites as well as the extension of the technique to flexible (hinge-bent) docking. This is demonstrated in the experiments performed as a lesson from our CAPRI experience.
KW - Binding site focusing
KW - CAPRI
KW - Flexible docking
KW - PatchDock
KW - Unbound docking
UR - http://www.scopus.com/inward/record.url?scp=0038237369&partnerID=8YFLogxK
U2 - 10.1002/prot.10397
DO - 10.1002/prot.10397
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AN - SCOPUS:0038237369
SN - 0887-3585
VL - 52
SP - 107
EP - 112
JO - Proteins: Structure, Function and Genetics
JF - Proteins: Structure, Function and Genetics
IS - 1
ER -