Cryo-electron microscopy of membrane proteins
Membrane proteins represent a large proportion of the proteome, but have characteristics
that are problematic for many methods in modern molecular biology (that have often been …
that are problematic for many methods in modern molecular biology (that have often been …
Computational methodologies for real-space structural refinement of large macromolecular complexes
The rise of the computer as a powerful tool for model building and refinement has
revolutionized the field of structure determination for large biomolecular systems. Despite …
revolutionized the field of structure determination for large biomolecular systems. Despite …
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
A novel method to flexibly fit atomic structures into electron microscopy (EM) maps using
molecular dynamics simulations is presented. The simulations incorporate the EM data as …
molecular dynamics simulations is presented. The simulations incorporate the EM data as …
Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography
Hybrid computational methods for combining structural data from different sources and
resolutions are becoming an essential part of structural biology, especially as the field …
resolutions are becoming an essential part of structural biology, especially as the field …
Refinement of protein structures into low-resolution density maps using rosetta
We describe a method based on Rosetta structure refinement for generating high-resolution,
all-atom protein models from electron cryomicroscopy density maps. A local measure of the …
all-atom protein models from electron cryomicroscopy density maps. A local measure of the …
Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps
Two structure determination methods, based on the molecular dynamics flexible fitting
(MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps …
(MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps …
iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates
Here, we employed the collective motions extracted from Normal Mode Analysis (NMA) in
internal coordinates (torsional space) for the flexible fitting of atomic-resolution structures …
internal coordinates (torsional space) for the flexible fitting of atomic-resolution structures …
Advances in the molecular dynamics flexible fitting method for cryo-EM modeling
Abstract Molecular Dynamics Flexible Fitting (MDFF) is an established technique for fitting
all-atom structures of molecules into corresponding cryo-electron microscopy (cryo-EM) …
all-atom structures of molecules into corresponding cryo-electron microscopy (cryo-EM) …
Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations
A methodology for flexible fitting of all-atom high-resolution structures into low-resolution
cryoelectron microscopy (cryo-EM) maps is presented. Flexibility of the modeled structure is …
cryoelectron microscopy (cryo-EM) maps is presented. Flexibility of the modeled structure is …
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches
Flexible fitting based on molecular dynamics simulation is a technique for structure modeling
from cryo-EM data. It has been utilized for nearly two decades, and while cryo-EM resolution …
from cryo-EM data. It has been utilized for nearly two decades, and while cryo-EM resolution …