Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding.
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ABSTRACT:
SUBMITTER: Watanabe YS
PROVIDER: S-EPMC5036648 | biostudies-literature | 2006
REPOSITORIES: biostudies-literature
Publications
Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding.
Watanabe Yukihisa S YS Fukunishi Yoshifumi Y Nakamura Haruki H
Biophysics (Nagoya-shi, Japan) 20060131
Molecular recognition is often mediated by flexible loops that have widely fluctuating structures and are sometimes disordered, but that form particular complex structures following ligand binding. In fact, many loop structures found in the PDB database are too flexible to be determined precisely. A new loop modeling method was therefore developed using force-biased multicanonical molecular dynamics with the implicit solvent model to generate an ensemble of putative loop structures with low free ...[more]
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