List of works - Florence Tama

3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.

scientific article published on 13 May 2013

Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning

scientific article published on 18 October 2018

Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization

scientific article

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

scientific article

Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP kinases to SPEECHLESS

scientific article published on 24 June 2019

Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth

scientific article published on 23 January 2019

Computational Investigation of the Conformational Dynamics in Tom20-Mitochondrial Presequence Tethered Complexes

scientific article published on 16 November 2018

Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps

scientific article published on 14 February 2020

Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition.

scientific article

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

scientific article

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

scientific article

Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations

scientific article published on 13 December 2018

Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis

scientific article published on 01 January 2005

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

scientific article

Editorial overview: Macromolecular assemblies

scientific article published on 01 April 2017

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

scientific article published on June 2006

Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.

scientific article published on August 2002

Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations

scientific article published on 10 October 2008

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

scientific article

Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.

scientific article published in April 2004

Gaussian mixture model for coarse-grained modeling from XFEL

scientific article published on 01 October 2018

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.

scientific article published on 27 September 2014

Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data

scientific article published on 01 January 2018

Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns.

scientific article

Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes.

scientific article published on 6 February 2014

Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging

scientific article

Mega-Dalton Biomolecular Motion Captured from Electron Microscopy Reconstructions

scientific article published on 01 February 2003

Model of the toxic complex of anthrax: responsive conformational changes in both the lethal factor and the protective antigen heptamer

scientific article

Molecular dynamics simulation shows large volume fluctuations of proteins

scientific article published on 01 January 2000

Molecular model of a soluble guanylyl cyclase fragment determined by small-angle X-ray scattering and chemical cross-linking

scientific article published on 15 February 2013

Network visualization of conformational sampling during molecular dynamics simulation.

scientific article published on 16 October 2013

Normal mode analysis with simplified models to investigate the global dynamics of biological systems.

scientific article

Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.

scientific article

Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data

scientific article

Phosphorylated Smooth Muscle Heavy Meromyosin Shows an Open Conformation Linked to Activation

scientific article

Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images

scientific article published on 05 August 2021

Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release

scientific article

Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins

scientific article published on June 2014

Ribosome motions modulate electrostatic properties

scientific article published in August 2004

Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

scientific article

Searching for 3D structural models from a library of biological shapes using a few 2D experimental images

scientific article published on 12 September 2018

Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution

scientific article published on 30 May 2018

Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition

scientific article

Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis ⬇️

scientific article published on September 17, 2010

Structure of the E. coli protein-conducting channel bound to a translating ribosome

scientific article

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

scientific article

The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy.

scientific article published on April 2005

The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus

scientific article published on May 2002

The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function

scientific article published on 01 January 2005

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

scientific article published on 3 November 2015

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL.

scientific article published on 14 June 2017

Three-dimensional structure of the anthrax toxin pore inserted into lipid nanodiscs and lipid vesicles

scientific article

Topology representing neural networks reconcile biomolecular shape, structure, and dynamics

article

List of works by Florence Tama

3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.

Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning

Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization

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

Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP kinases to SPEECHLESS

Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth

Computational Investigation of the Conformational Dynamics in Tom20-Mitochondrial Presequence Tethered Complexes

Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps

Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition.

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

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

Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations

Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

Editorial overview: Macromolecular assemblies

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.

Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations

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

Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.

Gaussian mixture model for coarse-grained modeling from XFEL

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.

Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data

Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns.

Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes.

Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging

Mega-Dalton Biomolecular Motion Captured from Electron Microscopy Reconstructions

Model of the toxic complex of anthrax: responsive conformational changes in both the lethal factor and the protective antigen heptamer

Molecular dynamics simulation shows large volume fluctuations of proteins

Molecular model of a soluble guanylyl cyclase fragment determined by small-angle X-ray scattering and chemical cross-linking

Network visualization of conformational sampling during molecular dynamics simulation.

Normal mode analysis with simplified models to investigate the global dynamics of biological systems.

Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.

Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data

Phosphorylated Smooth Muscle Heavy Meromyosin Shows an Open Conformation Linked to Activation

Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images

Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release

Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins

Ribosome motions modulate electrostatic properties

Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

Searching for 3D structural models from a library of biological shapes using a few 2D experimental images

Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution

Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition

Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis ⬇️

Structure of the E. coli protein-conducting channel bound to a translating ribosome

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy.

The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus

The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL.

Three-dimensional structure of the anthrax toxin pore inserted into lipid nanodiscs and lipid vesicles

Topology representing neural networks reconcile biomolecular shape, structure, and dynamics