MD movie

Protein folding of src SH3 domain by a Go model.

A cooperative and reversible folding-unfolding trajectory of src SH3 domain simulated by a C-alpha Go model. (Koga & Takada JMB 2001)

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Protein folding of fibronectin type III by a Go model.

A single folding event of fibronectin type III simulated by a C-alpha Go model. (Koga & Takada JMB 2001)

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Monte Carlo simulation for structure prediction.

A small globular protein, protein G, is simulated by the multicanonical-ensemble fragment-assembly MC method. (This is not a MD movie!) (Chikenji et al. JCP 2003)

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A rotary motion of F1-ATPase by a coarse-grained model simulation.

A rotary motion of F1-ATPase simulated via the always-bi-site scheme. (Koga & Takada PNAS 2006)

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Conformational transition between ligand-unbound and bound states of glutamine-binding protein.

Reversible transition between open and closed conformations of GBP simulated by the multiple-basin model. (Okazaki et al. PNAS 2006)

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Drug export and allosteric conformational change of multi-drug transporter.

Conformational change in a subunit that binds a drug (the bottom left subunit) induces the drug export and allosteric conformational changes in the other two subunits. (Yao et al. Nat Commun 2010)

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A transcription factor p53 sliding along non-specific duplex DNA

A tumor suppressor p53 needs to search its recognition element in very long genomic DNA. For the search, p53 can slide along DNA, of which process is simulated here. Interestingly, p53 uses its C-terminal flexible tail (drawn in red) for the sliding (Terakawa et al JACS 2012).