Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking.
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.
Schneidman-Duhovny
Dina
D
School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
Inbar
Yuval
Y
Polak
Vladimir
V
Shatsky
Maxim
M
Halperin
Inbal
I
Benyamini
Hadar
H
Barzilai
Adi
A
Dror
Oranit
O
Haspel
Nurit
N
Nussinov
Ruth
R
Wolfson
Haim J
HJ
D000465:Algorithms; D000906:Antibodies / Q000737:chemistry / Q000276:immunology; D000956:Antigens, Viral; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry / Q000276:immunology; D005098:Exotoxins / Q000737:chemistry / Q000378:metabolism; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000737:chemistry / Q000276:immunology; D046911:Macromolecular Substances; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry / Q000378:metabolism; D025941:Protein Interaction Mapping; D017346:Protein Serine-Threonine Kinases / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000737:chemistry / Q000378:metabolism; D000516:alpha-Amylases / Q000737:chemistry / Q000378:metabolism
D000906:Antibodies; D000956:Antigens, Viral; D001426:Bacterial Proteins; D036022:Capsid Proteins; D005098:Exotoxins; D019267:Hemagglutinin Glycoproteins, Influenza Virus; D046911:Macromolecular Substances; D008565:Membrane Proteins; D011506:Proteins; D016693:Receptors, Antigen, T-Cell, alpha-beta; C117980:SpeA protein, Streptococcus pyogenes; C061332:VP6 protein, Rotavirus; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C030182:phosphocarrier protein HPr; C110847:HPr kinase; D017346:Protein Serine-Threonine Kinases; D000516:alpha-Amylases