… Protein structure refinement during CASP11 by the Feig group was described. Molecular
dynamics simulations were … On average, modest refinement was achieved with some targets …

A method for the local refinement of protein structures that … and sampling via molecular
dynamics simulations with a … range for high-resolution protein structures. The method is …

… structure predictions and correct native experimental structures via molecular dynamics
computer simulations. … that structure refinement to experimental accuracy via simulation is indeed …

… We have demonstrated that meaningful high-resolution structure refinement of protein
structure can be achieved with careful MD simulations in modern molecular mechanical force …

… -based refinement, by applying long, all-atom MD simulations—two to three orders of magnitude
longer than previous attempts at all-atom MD-based refinement—to structure refinement …

… the use of molecular dynamics simulations performed using atomic-… refinement of protein
structures generated ab initio or based on homology. This study is based on a set of 15 proteins …

… the model structures with the experimental structures and it is different from ours to refine the
… method is now reliable and useful for structure refinement, if it is properly combined with an …

… protein structure refinement protocol for aqueous proteins to membrane proteins. We
compared sampling via MD in aqueous solvent, the standard protocol for soluble proteins, with …

… The new PREFMD protein structure refinement web server is described. The method is
based on a top-performing MD-based refinement protocol that was optimized to perform well at …

… In this work, we will systematically examine the ability of MD simulations to refine protein
structural models and check in particular the possibility of reshaping the middle-range funnel of …