Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach (Q26851157)

main subject

computational biology

0 references

1 reference

Lars Skjærven

1 reference

Nathalie Reuter

1 reference

Aurora Martinez

1 reference

language of work or name

1 reference

December 2011

1 reference

Future Medicinal Chemistry

published in

1 reference

1 reference

1 reference

2079-100

1 reference

A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis

cites work

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Dynamic personalities of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Functional aspects of protein flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Large-scale modulation of thermodynamic protein folding barriers linked to electrostatics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Application of a Theory of Enzyme Specificity to Protein Synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Can allosteric regulation be predicted from structure?

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Folding and binding cascades: dynamic landscapes and population shifts

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Folding funnels, binding funnels, and protein function

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Ligand binding and internal equilibiums in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Intrinsic motions along an enzymatic reaction trajectory

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

The activation mechanism of chemokine receptor CCR5 involves common structural changes but a different network of interhelical interactions relative to rhodopsin

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Direct discrimination between models of protein activation by single-molecule force measurements

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Allosteric proteins and cellular control systems

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Is allostery an intrinsic property of all dynamic proteins?

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

The structural basis of negative cooperativity: receptors and enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Allostery and cooperativity revisited

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Allosteric mechanisms of signal transduction

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

The origin of allosteric functional modulation: multiple pre-existing pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Protein states and proteinquakes

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Diffractive optics-based heterodyne-detected four-wave mixing signals of protein motion: from "protein quakes" to ligand escape for myoglobin.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Dynamics of a small globular protein in terms of low-frequency vibrational modes

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Monte Carlo sampling methods using Markov chains and their applications

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Molecular dynamics of biological macromolecules: a brief history and perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Protein structural transitions and their functional role

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Molecular dynamics and protein function

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Molecular dynamics simulations of biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Coarse-grained normal mode analysis in structural biology

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

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

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

All-atom empirical potential for molecular modeling and dynamics studies of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Molecular dynamics: survey of methods for simulating the activity of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Large conformational changes in proteins: signaling and other functions

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

The Amber biomolecular simulation programs

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

CHARMM: the biomolecular simulation program

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

The GROMOS software for biomolecular simulation: GROMOS05.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Scalable molecular dynamics with NAMD

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

A dynamic model for the allosteric mechanism of GroEL

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Steered molecular dynamics and mechanical functions of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Predicting slow structural transitions in macromolecular systems: Conformational flooding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Escaping free-energy minima

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Investigating reaction pathways in rare events simulations of antibiotics diffusion through protein channels

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Parallel tempering: theory, applications, and new perspectives

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Replica Monte Carlo simulation of spin glasses.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Computing time scales from reaction coordinates by milestoning

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

A Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Systems

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Anton, a special-purpose machine for molecular dynamics simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Long-timescale molecular dynamics simulations of protein structure and function.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

High-throughput all-atom molecular dynamics simulations using distributed computing.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Essential dynamics of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Can principal components yield a dimension reduced description of protein dynamics on long time scales?

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Analysis of domain motions by approximate normal mode calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

GroEL-GroES-mediated protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Chaperonin-mediated protein folding: using a central cavity to kinetically assist polypeptide chain folding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

The crystal structure of the bacterial chaperonin GroEL at 2.8 A

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Nested cooperativity in the ATPase activity of the oligomeric chaperonin GroEL.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

ATP-bound states of GroEL captured by cryo-electron microscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Conservation among HSP60 sequences in relation to structure, function, and evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Dynamics of allosteric transitions in GroEL.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

The allosteric mechanism of the chaperonin GroEL: a dynamic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Annealing function of GroEL: structural and bioinformatic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

The Energy Landscapes and Motions of Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Out-of-equilibrium conformational cycling of GroEL under saturating ATP concentrations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Anisotropy of fluctuation dynamics of proteins with an elastic network model

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Comparison of mode analyses at different resolutions applied to nucleic acid systems

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Protein structural variation in computational models and crystallographic data

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Toward a unified representation of protein structural dynamics in solution.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Maltose-binding protein: a versatile platform for prototyping biosensing

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Stochastic gating and drug-ribosome interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Target flexibility: an emerging consideration in drug discovery and design

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Normal mode analysis for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Complementarity of Structure Ensembles in Protein-Protein Binding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

The active-inactive transition of human thymidylate synthase: Targeted molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Harmonicity in slow protein dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Proteome-wide Analysis of Chaperonin-Dependent Protein Folding in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Crystal structure of the temperature-sensitive and allosteric-defective chaperonin GroELE461K

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

Flooding inGROMACS: Accelerated barrier crossings in molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

7 January 2021

Computer simulations of protein folding by targeted molecular dynamics

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

7 January 2021

Conformational changes in the chaperonin GroEL: new insights into the allosteric mechanism

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

7 January 2021

Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

7 January 2021

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

7 January 2021

A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

7 January 2021

Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES.

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

7 January 2021

The pathway of allosteric control as revealed by hemoglobin intermediate states.

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

7 January 2021

Two-state allosteric behavior in a single-domain signaling protein

1 reference

https://api.crossref.org/works/10.4155%2FFMC.11.159

7 January 2021

Identifiers

DOI

10.4155/FMC.11.159

0 references

PubMed publication ID

22098354

1 reference