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Experimental measurements of biomolecular forces are ever-increasing in resolution, which calls for a convenient way of calculating forces as free energy gradients in simulations. While it is possible to first calculate the free energy landscape and take the gradient, free energy simulations typically require very extensive sampling time. Here, a quick and dirty method of calculating force at a given...
The AAA+ (ATPase Associated with various cellular Activities) machinery represents an extremely successful and widely used design plan for biological motors. Recently found crystal structures are beginning to reveal nucleotide-dependent conformational changes in the canonical hexameric rings of the AAA+ motors. However, the physical mechanism by which ATP binding on one subunit allosterically propagates...
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