Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps
出版年份 2016 全文链接
标题
Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps
作者
关键词
-
出版物
eLife
Volume 5, Issue -, Pages -
出版商
eLife Sciences Organisation, Ltd.
发表日期
2016-07-07
DOI
10.7554/elife.16105
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating
- (2016) Doreen Matthies et al. CELL
- Advances in the molecular dynamics flexible fitting method for cryo-EM modeling
- (2016) Ryan McGreevy et al. METHODS
- Single-Particle Cryo-EM at Crystallographic Resolution
- (2015) Yifan Cheng CELL
- Membrane protein structural biology using X-ray free electron lasers
- (2015) Richard Neutze et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Improved cryoEM-Guided Iterative Molecular Dynamics–Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction
- (2015) Steffen Lindert et al. Journal of Chemical Theory and Computation
- Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles
- (2015) Abhishek Singharoy et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Mechanistic insights into the recycling machine of the SNARE complex
- (2015) Minglei Zhao et al. NATURE
- 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
- An atomic structure of human γ-secretase
- (2015) Xiao-chen Bai et al. 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
- EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
- (2015) Benjamin A Barad et al. NATURE METHODS
- 2.2 A resolution cryo-EM structure of -galactosidase in complex with a cell-permeant inhibitor
- (2015) A. Bartesaghi et al. SCIENCE
- Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis
- (2015) Boon Chong Goh et al. STRUCTURE
- Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud
- (2015) Michael A Cianfrocco et al. eLife
- GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting
- (2014) John E. Stone et al. FARADAY DISCUSSIONS
- Three-dimensional structure of human γ-secretase
- (2014) Peilong Lu et al. NATURE
- Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain
- (2014) Qufei Li et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Structure of -galactosidase at 3.2-A resolution obtained by cryo-electron microscopy
- (2014) A. Bartesaghi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals
- (2014) Antonija Kuzmanic et al. Nature Communications
- A structural model of the active ribosome-bound membrane protein insertase YidC
- (2014) Stephan Wickles et al. eLife
- xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures
- (2014) Ryan McGreevy et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD
- (2013) Wei Jiang et al. COMPUTER PHYSICS COMMUNICATIONS
- Electron Density Sharpening as a General Technique in Crystallographic Studies
- (2013) Chang Liu et al. JOURNAL OF MOLECULAR 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
- Epitope Fluctuations in the Human Papillomavirus Are Under Dynamic Allosteric Control: A Computational Evaluation of a New Vaccine Design Strategy
- (2013) Abhishek Singharoy et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
- (2013) Gongpu Zhao et al. NATURE
- Structure of the TRPV1 ion channel determined by electron cryo-microscopy
- (2013) Maofu Liao et al. NATURE
- Quantifying the local resolution of cryo-EM density maps
- (2013) Alp Kucukelbir et al. NATURE METHODS
- Improved low-resolution crystallographic refinement with Phenix and Rosetta
- (2013) Frank DiMaio et al. NATURE METHODS
- Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
- (2013) Xueming Li et al. NATURE METHODS
- Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
- (2012) Robert B. Best et al. Journal of Chemical Theory and Computation
- A pseudoatomic model of the COPII cage obtained from cryo-electron microscopy and mass spectrometry
- (2012) Alex J Noble et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Improving the Accuracy of Macromolecular Structure Refinement at 7 Å Resolution
- (2012) Axel T. Brunger et al. STRUCTURE
- REFMAC5 for the refinement of macromolecular crystal structures
- (2011) Garib N. Murshudov et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Parallel Generalized Born Implicit Solvent Calculations with NAMD
- (2011) David E. Tanner et al. Journal of Chemical Theory and Computation
- Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy
- (2011) Anna-Clare Milazzo et al. JOURNAL OF STRUCTURAL BIOLOGY
- Cryo-EM structure of the ribosome–SecYE complex in the membrane environment
- (2011) Jens Frauenfeld et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Symmetry-Restrained Flexible Fitting for Symmetric EM Maps
- (2011) Kwok-Yan Chan et al. STRUCTURE
- PHENIX: a comprehensive Python-based system for macromolecular structure solution
- (2010) Paul D. Adams et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
- (2010) Jeffery B. Klauda et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Applications of the molecular dynamics flexible fitting method
- (2010) Leonardo G. Trabuco et al. JOURNAL OF STRUCTURAL BIOLOGY
- Super-resolution biomolecular crystallography with low-resolution data
- (2010) Gunnar F. Schröder et al. NATURE
- Challenges in protein-folding simulations
- (2010) Peter L. Freddolino et al. Nature Physics
- MolProbity: all-atom structure validation for macromolecular crystallography
- (2009) Vincent B. Chen et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Protein-Induced Membrane Curvature Investigated through Molecular Dynamics Flexible Fitting
- (2009) Jen Hsin et al. BIOPHYSICAL JOURNAL
- Structural model and excitonic properties of the dimeric RC–LH1–PufX complex from Rhodobacter sphaeroides
- (2009) Melih Şener et al. CHEMICAL PHYSICS
- Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography
- (2009) Leonardo G. Trabuco et al. METHODS
- SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs
- (2009) Tanvir R Shaikh et al. Nature Protocols
- Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis
- (2009) E. Villa et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Flexible Fitting of High-Resolution X-Ray Structures into Cryoelectron Microscopy Maps Using Biased Molecular Dynamics Simulations
- (2008) Marek Orzechowski et al. BIOPHYSICAL JOURNAL
- Damped-Dynamics Flexible Fitting
- (2008) Julio A. Kovacs et al. BIOPHYSICAL JOURNAL
- CHARMM-GUI: A web-based graphical user interface for CHARMM
- (2008) Sunhwan Jo et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Sharpening high resolution information in single particle electron cryomicroscopy
- (2008) J.J. Fernández et al. JOURNAL OF STRUCTURAL BIOLOGY
- Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
- (2008) Gerrit Langer et al. Nature Protocols
- 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
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreDiscover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversation