記事
Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images
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CiNii Research
Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images
- 資料種別
- 記事
- 著者
- Bhaskar Dasguptaほか
- 出版者
- Elsevier BV
- 出版年
- 2020-02
- 資料形態
- デジタル
- 掲載誌名
- Biochimica et Biophysica Acta (BBA) - General Subjects 1864 2
- 掲載ページ
- p.129420-
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デジタル
- 資料種別
- 記事
- タイトル
- 出版年月日等
- 2020-02
- 出版年(W3CDTF)
- 2020-02
- タイトル(掲載誌)
- Biochimica et Biophysica Acta (BBA) - General Subjects
- 巻号年月日等(掲載誌)
- 1864 2
- 掲載巻
- 1864
- 掲載号
- 2
- 掲載ページ
- 129420-
- 掲載年月日(W3CDTF)
- 2020-02
- ISSN(掲載誌)
- 03044165
- 出版事項(掲載誌)
- Elsevier BV
- 対象利用者
- 一般
- DOI
- 10.1016/j.bbagen.2019.129420
- 作成日(W3CDTF)
- 2019-08-28
- 著作権情報
- https://www.elsevier.com/tdm/userlicense/1.0/
- 関連情報(URI)
- 参照
- Spatiotemporal resolution in high-speed atomic force microscopy for studying biological macromolecules in actionBioAFMviewer software for simulation atomic force microscopy of molecular structures and conformational dynamicsEnd-to-end differentiable blind tip reconstruction for noisy atomic force microscopy imagesReconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy ImagesRigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structureDevelopment of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series imagesInferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular SimulationsProtein dynamics by the combination of high-speed AFM and computational modelingA hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data
- 参照
- High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsinGuide to video recording of structure dynamics and dynamic processes of proteins by high-speed atomic force microscopyHigh-speed atomic force microscopy coming of ageNew tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)De Novo modeling in cryo-EM density maps with PathwalkingAn overview of the biophysical applications of atomic force microscopyFoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profilesIntegrative structure and functional anatomy of a nuclear pore complexDetermining the architectures of macromolecular assembliesStructural Changes in Bacteriorhodopsin in Response to Alternate Illumination Observed by High‐Speed Atomic Force MicroscopyVideo imaging of walking myosin V by high-speed atomic force microscopyGaussian mixture model for coarse-grained modeling from XFELUCSF Chimera—A visualization system for exploratory research and analysisMature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamicsReal-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopyRole of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and DynamicsNormal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EMHigh-Resolution Comparative Modeling with RosettaCMNormal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules toward SAXS DataSubstrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase FunctionA Cas9–guide RNA complex preorganized for target DNA recognitionCharacterization of the motion of membrane proteins using high-speed atomic force microscopyHigh-Speed AFM and Applications to Biomolecular SystemsFlexible fitting to cryo‐EM density map using ensemble molecular dynamics simulationsHybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patternsHigh-Speed Atomic Force Microscopy Techniques for Observing Dynamic Biomolecular ProcessesProtein Structure Fitting and Refinement Guided by Cryo-EM DensityScanning Tunneling Microscopy and Atomic Force Microscopy: Application to Biology and TechnologyThe Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRETIntegrative Structural Investigation on the Architecture of Human Importin4_Histone H3/H4_Asf1a Complex and Its Histone H3 Tail BindingDockAFM: benchmarking protein structures by docking under AFM topographsAccurate Flexible Fitting of High-Resolution Protein Structures to Small-Angle X-Ray Scattering Data Using a Coarse-Grained Model with Implicit Hydration ShellFlexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular DynamicsConsensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM dataStructural basis of PAM-dependent target DNA recognition by the Cas9 endonucleaseMolecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy mapsThe<i>Small Angle Scattering ToolBox</i>(<i>SASTBX</i>): an open-source software for biomolecular small-angle scatteringWAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics<i>Fast-SAXS-pro</i>: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexesMethods for SAXS‐Based Structure Determination of Biomolecular ComplexesStructures of a CRISPR-Cas9 R-loop complex primed for DNA cleavageMultiple Subunit Fitting into a Low-Resolution Density Map of a Macromolecular Complex Using a Gaussian Mixture ModelMolecular Model of a Soluble Guanylyl Cyclase Fragment Determined by Small-Angle X-ray Scattering and Chemical Cross-LinkingDe novo protein structure determination from near-atomic-resolution cryo-EM mapsStructures of Cas9 Endonucleases Reveal RNA-Mediated Conformational ActivationTools for integrated sequence-structure analysis with UCSF ChimeraIterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular ComplexesGo hybrid: EM, crystallography, and beyondPutting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular AssembliesSAXS Data Alone can Generate High-Quality Models of Protein-Protein ComplexesTwo crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocaseDetermining Complex Structures using Docking Method with Single Particle Scattering DataAtomic force microscopy as a multifunctional molecular toolbox in nanobiotechnologyiMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinatesBayesian refinement of protein structures and ensembles against SAXS data using molecular dynamicsMD–SAXS method with nonspherical boundariesComputational Reconstruction of Multidomain Proteins Using Atomic Force Microscopy DataBiased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy mapsA practical guide to small angle X‐ray scattering (SAXS) of flexible and intrinsically disordered proteinsTheoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational dockingMacromolecular docking restrained by a small angle X-ray scattering profileUsing Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions
- 連携機関・データベース
- 国立情報学研究所 : CiNii Research
- 提供元機関・データベース
- Crossref科学研究費助成事業データベース科学研究費助成事業データベースCrossrefCrossrefCrossrefCrossrefCrossrefCrossrefCrossrefCrossrefCrossref