Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.

By Leonardo G. Trabuco, Elizabeth Villa, K. Mitra, Joachim Frank, Klaus Schulten. Structure, 2008

920 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology, Structural Biology

View Paper: https://www.semanticscholar.org/paper/1489b6d643636f609a5182f38efa93b615934ac1

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Atomic and Molecular Physics, and Optics

In Molecular Biology

In Structural Biology

Citations in the corpus

UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System (2011, methodology): “Methods of ﬂexible ﬁt-ting include molecular dynamics (Trabuco et al., 2008), Monte Carlo (Topf et al., 2008), normal mode analysis (Tama et al., 2004), and morphing (Wriggers, 2010; Wriggers and Chacón, 2001).”
CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps (2023, background): “Each subunit was then subjected to a fitting force which is simply the negative gradient of the cryoEM map 21 , whilst strong harmonic restraints maintain the overall geometry of the subunit.”
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps (2018, methodology): “Recently, I demonstrated the use of interactive MDFF simulations to improve models built into challenging low-resolution crystallographic maps (Croll et al., 2016; Croll & Andersen, 2016; Focht et al., 2017).”
Discovery Through the Computational Microscope (2009, neutral): “…data, as in the case of atomic force microscopy studies (Rief and Grubmüller, 2002; Zlatanova and van Holde, 2006; Sotomayor and Schulten, 2007; Prevost et al., 2009) or the analysis of macromolecular structures using electron microscopy (Saibil, 2000; Frank, 2006; Trabuco et al., 2008).”
Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, methodology): “It should be noted that other software tools are available for the ﬁtting and reﬁne-ment of atomic models into cryo-EM maps, including DireX (Schro¨der et al. , 2007), MDFF (Trabuco et al. , 2008), Cryo-Fit (Kirmizialtin et al. , 2015), Rosetta (Wang et al. , 2016) and phenix.real_space_reﬁne (Afoni”
De novo computational RNA modeling into cryoEM maps of large ribonucleoprotein complexes (2018, positive): “4 structures of alternative conformational states, into density maps ranging from low- to highresolution and has been successfully applied to large RNP assemblies such as the ribosome to generate accurate atomic models of different functional states [24].”