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performed using SYBYL 7.3.4 (Tripos Discovery Informatics, St.
Louis, MO) installed on a Dell desktop workstation equipped with
a 1.86 GHz Intel Xeon processor and the Red Hat Enterprise Linux
(version 4) operating system. The 3D coordinates of rabbit muscle
R-actin complex with latrunculin A (1) were retrieved from the
Protein Data Bank (PDB code: 1esv). The selected structure is of
the best 3D resolution (2.0 Å). The protein structure was utilized in
subsequent docking experiments without energy minimization.
Explicit water molecules were removed from the structure. Chemical
structures of 1-6 were drawn in SYBYL 7.3.4 and assigned
Gasteiger partial charges and energy minimized using Energy Force
Field. Docking simulations of structures 1-6 were carried out using
SurFlex-Dock (version 2.1). SurFlex-Dock identifies the active site
of the protein and constructs a docking target (protomol) to which
molecules match. Protmol was generated by the ligand-based
method, setting the Threshold and Bloat parameters as default value
(0.5 and 0.0, respectively).
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Acknowledgment. This investigation was made possible through
the support of NIH grant number P20RR16456 from the BRIN Program
of the National Center for Research Resources, grant R01CA96534
(G.V.S.), and grant CA98787 (D.G.N., Y.-D.Z.). Its contents are solely
the responsibility of the authors and do not necessarily represent the
official views of NIH. Louisiana Board of Regents grant LEQSF(2007-
08)-ENH-TR-80 is acknowledged for the support of the purchase of
the NMR probe.
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NP070587W