Sentence examples for flexible fitting from inspiring English sources

Particularly, we concentrate on two methods in this Review: (a) normal mode flexible fitting (NMFF) for structural refinement into EM maps; and (b) temperature-accelerated molecular dynamics (TAMD) for conformational exploration and flexible fitting.

The instrumentation must be very flexible fitting the set-up for both investigations.

To obtain deeper insights into the architecture and function of HsTPPII, we have created a pseudoatomic structure of the HsTPPII spindle using a comparative model of HsTPPII dimers and molecular dynamics flexible fitting.

Future directions will include the improvement of the scoring as well as the extension with flexible fitting.

DOI: http://dx.doi.org/10.7554/eLife.00411.011 10.7554/eLiFigure11.012 Figure 5. Flexible fitting by MDFF focusing on RF3 conformation and interaction with RF1.

We introduced interpolation as an efficient and easy-to-use alternative to constrained MD, with the goal of making the flexible fitting techniques available to non-expert users.

We originally developed our flexible fitting techniques in collaboration with Seth Darst, whose laboratory determined the structure of Escherichia coli core RNAP by cryo-EM and image processing of helical crystals to a resolution of 15 Å.

Molecular dynamics flexible fitting (MDFF) (Trabuco et al., 2009) was used to refine the complex structure by incorporating the EM density map as an external potential into MD sampling.

This may be viewed as computationally inefficient compared to REML estimates (for example, as implemented in WOMBAT [ 14]); however, Bayesian MCMC methods are appealing since they allow for more flexible fitting to complex models which is advantageous in the genetic analysis of non-normal data [ 18].

Root-mean-square deviation plots describing changes in the structures as well as changes in the cross-correlation coefficient between structures and density maps over the course of the MDFF fits are presented in Figure 4 figure supplement 1. 10.7554/eLife.00411.010 Figure 4. Flexible fitting by MDFF focusing on RF1 conformation and interactions.

(4) Rd3: The Rs1 structure was rigidly fitted, and flexible fitting was applied using three rigid bodies (the three domains) for ten iterations.