Coarse and reliable geometric alignment for protein docking.
We present an efficient algorithm for generating a small set of coarse alignments between interacting proteins using meaningful features on their surfaces. The proteins are treated as rigid bodies, but the results are more generally useful as the produced configurations can serve as input to local improvement algorithms that allow for protein flexibility. We apply our algorithm to a diverse set of protein complexes from the Protein Data Bank, demonstrating the effectivity of our algorithm, both for bound and for unbound protein docking problems.
Wang
Y
Y
Department of Computer Science, Duke University, Durham, North Carolina, USA.
Agarwal
P K
PK
Brown
P
P
Edelsbrunner
H
H
Rudolph
J
J
D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D012984:Software
D011506:Proteins