The 150 top-scoring topologies were then symmetrized and subjected to another round of EM-fold refinement against the density map.
We incorporated RNA-seq quantification of total mRNA to identify expression-weighted Ago footprints, and developed a microRNA regulatory element (MRE) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone.
This refinement of the computational approach using our experimental data on RISC footprints resulted in 125,949 unique and high confidence miRNA/mRNA pairs, which is a greater than 20-fold refinement of the results obtained from computational target prediction alone.
The "Protein Folding" and "Refinement" tutorials in the supplement cover many aspects of this protocol.
We provide six tutorials that demonstrate basic usage of R osetta: (1) protein folding, (2) refinement, (3) loop modeling, (4) protein−protein docking, (5) small molecule docking, and (6) protein design.
We have analysed the transition state of folding of the four-helix FF domain from HYPA/FBP11 by high-resolution experiment and simulation as part of a continuing effort to understand the principles of folding and the refinement of predictive methods.
The other one is MEA, maximum expected accuracy folding, which is a recent refinement of MFE folding.
While recent progress has demonstrated promising use of the structure-based iteration as driven by ab initio modeling in both fold-recognition and structure refinement procedures, the development of efficient ab initio folding algorithms will remain a major theme in the field and should have important impacts on all aspects of protein structure predictions.
The occurrence of the βαβ motif in a large number of protein families [3], [20] suggests that the N-terminal capping of β-strands by βα-hairpin clamps, akin to the analogous N-capping of α-helices [9], [10], may be a useful property for the refinement of protein fold prediction and for engineering stability in βα-repeat proteins.
This enabled automatic model building and manual rebuilding and refinement, using 2-fold non-crystallographic symmetry, to produce a high confidence structure, refined at 3.2 Å resolution with good R-factors and geometry (Table 1).
In general, RNA folding is thought to be hierarchical in nature [ 1, 2], whereby a stable secondary structure forms first and subsequently there is a refinement to the tertiary fold.
