Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations

Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure

(2016) Charles H. Greenberg et al.   JOURNAL OF STRUCTURAL BIOLOGY

Advances in the molecular dynamics flexible fitting method for cryo-EM modeling

(2016) Ryan McGreevy et al.   METHODS

Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment

(2016) Agnel Praveen Joseph et al.   METHODS

Near-atomic resolution visualization of human transcription promoter opening

(2016) Yuan He et al.   NATURE

Force-producing ADP state of myosin bound to actin

(2016) Sarah F. Wulf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

(2016) Abhishek Singharoy et al.   eLife

A Primer to Single-Particle Cryo-Electron Microscopy

(2015) Yifan Cheng et al.   CELL

Numerical geometry of map and model assessment

(2015) Willy Wriggers et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structural basis for stop codon recognition in eukaryotes

(2015) Alan Brown et al.   NATURE

Structure of the E. coli ribosome–EF-Tu complex at

(2015) Niels Fischer et al.   NATURE

The revolution will not be crystallized: a new method sweeps through structural biology

(2015) Ewen Callaway   NATURE

Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement

(2015) Frank DiMaio et al.   NATURE METHODS

Error-prone chromosome-mediated spindle assembly favors chromosome segregation defects in human oocytes

(2015) Z. Holubcova et al.   SCIENCE

How cryo-EM is revolutionizing structural biology

(2015) Xiao-chen Bai et al.   TRENDS IN BIOCHEMICAL SCIENCES

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

(2015) Jaewoon Jung et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Single-particle cryo-electron microscopy of macromolecular complexes

(2015) Georgios Skiniotis et al.   Microscopy

Function and dynamics of macromolecular complexes explored by integrative structural and computational biology

(2014) Michael D Purdy et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle

(2014) Christoph Leidig et al.   Nature Communications

Structural modeling from electron microscopy data

(2014) José Ramón López-Blanco et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Enhanced Sampling and Overfitting Analyses in Structural Refinement of Nucleic Acids into Electron Microscopy Maps

(2013) Harish Vashisth et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data

(2013) Aqeel Ahmed et al.   JOURNAL OF STRUCTURAL BIOLOGY

Targeted conformational search with map-restrained self-guided Langevin dynamics: Application to flexible fitting into electron microscopic density maps

(2013) Xiongwu Wu et al.   JOURNAL OF STRUCTURAL BIOLOGY

iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates

(2013) José Ramón Lopéz-Blanco et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structure of the TRPV1 ion channel determined by electron cryo-microscopy

(2013) Maofu Liao et al.   NATURE

Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome

(2013) Samuel Coulbourn Flores   NUCLEIC ACIDS RESEARCH

Equilibrium Sampling Approach to the Interpretation of Electron Density Maps

(2013) Andreas Vitalis et al.   STRUCTURE

Conventions and workflows for usingSitus

(2012) Willy Wriggers   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Go hybrid: EM, crystallography, and beyond

(2012) Gabriel C Lander et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Using Enhanced Sampling and Structural Restraints to Refine Atomic Structures into Low-Resolution Electron Microscopy Maps

(2012) Harish Vashisth et al.   STRUCTURE

Consensus among flexible fitting approaches improves the interpretation of cryo-EM data

(2011) Aqeel Ahmed et al.   JOURNAL OF STRUCTURAL BIOLOGY

Excited states of ribosome translocation revealed through integrative molecular modeling

(2011) P. C. Whitford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

(2010) Andreas H. Ratje et al.   NATURE

Inferential Optimization for Simultaneous Fitting of Multiple Components into a CryoEM Map of Their Assembly

(2009) Keren Lasker et al.   JOURNAL OF MOLECULAR BIOLOGY

Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps

(2009) Ivan Grubisic et al.   JOURNAL OF STRUCTURAL BIOLOGY

Flexible Fitting of High-Resolution X-Ray Structures into Cryoelectron Microscopy Maps Using Biased Molecular Dynamics Simulations

(2008) Marek Orzechowski et al.   BIOPHYSICAL JOURNAL

Multiple Subunit Fitting into a Low-Resolution Density Map of a Macromolecular Complex Using a Gaussian Mixture Model

(2008) Takeshi Kawabata   BIOPHYSICAL JOURNAL

YUP.SCX: Coaxing atomic models into medium resolution electron density maps

(2008) Robert K.-Z. Tan et al.   JOURNAL OF STRUCTURAL BIOLOGY

Protein Structure Fitting and Refinement Guided by Cryo-EM Density

(2008) Maya Topf et al.   STRUCTURE

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE

Fitting Low-Resolution Cryo-EM Maps of Proteins Using Constrained Geometric Simulations

(2007) Craig C. Jolley et al.   BIOPHYSICAL JOURNAL

Coarse-grained models of protein folding: toy models or predictive tools?

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY

The origins of asymmetry in the folding transition states of protein L and protein G

(2002) John Karanicolas et al.   PROTEIN SCIENCE