4.2 Article

Cryo-Electron Microscopy Modeling by the Molecular Dynamics Flexible Fitting Method

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。
Article Biochemical Research Methods

Stereochemical errors and their implications for molecular dynamics simulations

Eduard Schreiner et al.

BMC BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Structural insights into cognate versus near-cognate discrimination during decoding

Xabier Agirrezabala et al.

EMBO JOURNAL (2011)

Article Biochemistry & Molecular Biology

4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus

Rui Zhang et al.

EMBO JOURNAL (2011)

Article Chemistry, Physical

Parallel Generalized Born Implicit Solvent Calculations with NAMD

David E. Tanner et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Biochemistry & Molecular Biology

Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome

Thomas Becker et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Cryo-EM structure of the ribosome-SecYE complex in the membrane environment

Jens Frauenfeld et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Regulation by interdomain communication of a headful packaging nuclease from bacteriophage T4

Manjira Ghosh-Kumar et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Multidisciplinary Sciences

Role of SNX16 in the Dynamics of Tubulo-Cisternal Membrane Domains of Late Endosomes

Ben Brankatschk et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy

Qiang Guo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemistry & Molecular Biology

Molecular dynamics of EF-G during translocation

Wen Li et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Symmetry-Restrained Flexible Fitting for Symmetric EM Maps

Kwok-Yan Chan et al.

STRUCTURE (2011)

Article Virology

Near-atomic resolution cryo-EM for molecular virology

Corey F. Hryc et al.

CURRENT OPINION IN VIROLOGY (2011)

Article Biochemistry & Molecular Biology

Visualizing the transfer-messenger RNA as the ribosome resumes translation

Jie Fu et al.

EMBO JOURNAL (2010)

Article Biochemistry & Molecular Biology

Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals

Richard K. Hite et al.

EMBO JOURNAL (2010)

Article Biochemistry & Molecular Biology

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

Gong-Hong Wei et al.

EMBO JOURNAL (2010)

Article Biochemistry & Molecular Biology

Backbone Model of an Aquareovirus Virion by Cryo-Electron Microscopy and Bioinformatics

Lingpeng Cheng et al.

JOURNAL OF MOLECULAR BIOLOGY (2010)

Article Biochemistry & Molecular Biology

The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle

Leonardo G. Trabuco et al.

JOURNAL OF MOLECULAR BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Structural Basis for Translational Stalling by Human Cytomegalovirus and Fungal Arginine Attenuator Peptide

Shashi Bhushan et al.

MOLECULAR CELL (2010)

Article Multidisciplinary Sciences

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy

Niels Fischer et al.

NATURE (2010)

Article Multidisciplinary Sciences

Mechanism of folding chamber closure in a group II chaperonin

Junjie Zhang et al.

NATURE (2010)

Article Biochemical Research Methods

Cryo-EM of macromolecular assemblies at near-atomic resolution

Matthew L. Baker et al.

NATURE PROTOCOLS (2010)

Article Biochemistry & Molecular Biology

Conformational change of flagellin for polymorphic supercoiling of the flagellar filament

Saori Maki-Yonekura et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)

Article Biochemistry & Molecular Biology

α-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel

Shashi Bhushan et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)

Article Multidisciplinary Sciences

Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome

Jean-Paul Armache et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

The actin-myosin interface

Michael Lorenz et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemistry & Molecular Biology

Generating stereochemically acceptable protein pathways

Daniel W. Farrell et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Recognition of the Regulatory Nascent Chain TnaC by the Ribosome

Leonardo G. Trabuco et al.

STRUCTURE (2010)

Article Biochemistry & Molecular Biology

Formation of Salt Bridges Mediates Internal Dimerization of Myosin VI Medial Tail Domain

HyeongJun Kim et al.

STRUCTURE (2010)

Article Biochemical Research Methods

Use of thallium to identify monovalent cation binding sites in GroEL

Philip D. Kiser et al.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2009)

Article Biochemistry & Molecular Biology

GTPase activation of elongation factor EF-Tu by the ribosome during decoding

Jan-Christian Schuette et al.

EMBO JOURNAL (2009)

Article Biochemistry & Molecular Biology

Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome

Rebecca M. Voorhees et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Multidisciplinary Sciences

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

Elizabeth Villa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Structural Insight into Nascent Polypeptide Chain-Mediated Translational Stalling

Birgit Seidelt et al.

SCIENCE (2009)

Article Biochemistry & Molecular Biology

Regulation of the Protein-Conducting Channel by a Bound Ribosome

James Gumbart et al.

STRUCTURE (2009)

Review Biochemistry & Molecular Biology

Macromolecular modeling with Rosetta

Rhiju Das et al.

ANNUAL REVIEW OF BIOCHEMISTRY (2008)

Article Multidisciplinary Sciences

Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction

Xing Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemistry & Molecular Biology

De novo backbone trace of GroEL from single particle electron cryomicroscopy

Steven J. Ludtke et al.

STRUCTURE (2008)

Article Biochemistry & Molecular Biology

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

Leonardo G. Trabuco et al.

STRUCTURE (2008)

Article Biochemistry & Molecular Biology

Comparison of multiple amber force fields and development of improved protein backbone parameters

Viktor Hornak et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes

NA Ranson et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2006)

Review Chemistry, Multidisciplinary

Scalable molecular dynamics with NAMD

JC Phillips et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Review Physics, Multidisciplinary

Protein crystallography at subatomic resolution

T Petrova et al.

REPORTS ON PROGRESS IN PHYSICS (2004)

Article Biochemical Research Methods

Introduction to macromolecular refinement

DE Tronrud

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)