Lista de obras - Robert B. Best - Dominio Público Uruguay

(Ala)(4)-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters

artículo científico publicado en 2012

A "slow" protein folds quickly in the end.

artículo científico publicado en 2013

A microscopic model for gas diffusion dynamics in a [NiFe]-hydrogenase

artículo científico publicado en 2011

A mutant chaperonin with rearranged inter-ring electrostatic contacts and temperature-sensitive dissociation

artículo científico publicado en 2004

A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations

artículo científico publicado en 2012

A simple method for probing the mechanical unfolding pathway of proteins in detail

artículo científico publicado en 2002

A small single-domain protein folds through the same pathway on and off the ribosome

article published in the Proceedings of the National Academy of Sciences of the United States of America

Aerobic damage to [FeFe]-hydrogenases: activation barriers for the chemical attachment of O2.

artículo científico publicado en 2014

Are current molecular dynamics force fields too helical?

artículo científico publicado en 2008

Atomistic insights into rhodopsin activation from a dynamic model

artículo científico publicado en 2008

Atomistic mechanism of transmembrane helix association

artículo científico publicado en 2020

Atomistic molecular simulations of protein folding ⬇️

artículo científico publicado el 17 de enero de 2012

Balance between α and β Structures in Ab Initio Protein Folding

scientific article published on 01 July 2010

Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

artículo científico publicado en 2014

Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association

artículo científico publicado en 2018

Binding-induced folding of a natively unstructured transcription factor.

artículo científico publicado en 2008

Biochemistry. Unfolding the secrets of calmodulin

artículo científico publicado en 2009

Bootstrapping new protein folds

artículo científico publicado en 2014

Characterization of the residual structure in the unfolded state of the Δ131Δ fragment of staphylococcal nuclease

article

Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations

artículo científico publicado en 2007

Co-Evolutionary Fitness Landscapes for Sequence Design

article

Comment on "Force-Clamp Spectroscopy Monitors the Folding Trajectory of a Single Protein"

artículo científico publicado en 2005

Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water"

scientific article published on 01 August 2018

Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations

artículo científico publicado en 2013

Complex energy landscape of a giant repeat protein

artículo científico publicado en 2013

Computer Folding of RNA Tetraloops? Are We There Yet?

artículo científico publicado en 2013

Coordinate-dependent diffusion in protein folding

artículo científico publicado en 2009

Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions"

scientific article published on 19 December 2019

Correction to Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

artículo científico publicado en 2015

Correction to Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin

scientific article published on 30 April 2018

Correction to Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data

artículo científico publicado en 2016

Cotranslational folding cooperativity of contiguous domains of α-spectrin

artículo científico publicado en 2020

Crosstalk between the protein surface and hydrophobic core in a core-swapped fibronectin type III domain

artículo científico publicado en 2007

Cyclic N-terminal loop of amylin forms non amyloid fibers

artículo científico publicado en 2013

Dependence of internal friction on folding mechanism

artículo científico publicado en 2015

Dependence of protein folding stability and dynamics on the density and composition of macromolecular crowders

artículo científico publicado en 2010

Designing an extracellular matrix protein with enhanced mechanical stability

artículo científico publicado en 2007

Determination of protein structures consistent with NMR order parameters

artículo científico publicado en 2004

Diffusion models of protein folding ⬇️

artículo científico publicado el 15 de agosto de 2011

Diffusive Dynamics of Contact Formation in Disordered Polypeptides ⬇️

artículo científico publicado en 2016

Diffusive Model of Protein Folding Dynamics with Kramers Turnover in Rate

artículo científico publicado en 2006

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

artículo científico publicado en 2014

Disordered RNA chaperones can enhance nucleic acid folding via local charge screening

artículo científico publicado en 2019

Effect of interactions with the chaperonin cavity on protein folding and misfolding

artículo científico publicado en 2013

Effects of interactions with the GroEL cavity on protein folding rates

artículo científico publicado en 2013

Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations

artículo científico publicado en 2015

Engineering folding dynamics from two-state to downhill: application to λ-repressor

artículo científico publicado en 2013

Evidence for a partially structured state of the amylin monomer

artículo científico publicado en 2009

Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties

artículo científico publicado en 2019

Exploring the sequence fitness landscape of a bridge between protein folds

artículo científico publicado en 2020

Folding Kinetics and Unfolded State Dynamics of the GB1 Hairpin from Molecular Simulation

artículo científico publicado en 2013

Folding and binding: when the force is against you.

artículo científico publicado en 2013

Folding pathway of an Ig domain is conserved on and off the ribosome

article published in the Proceedings of the National Academy of Sciences of the United States of America

Force-Induced Change in Protein Unfolding Mechanism: Discrete or Continuous Switch?

article

Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign

artículo científico publicado en 2012

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

artículo científico publicado en 2011

Hidden complexity in the mechanical properties of titin

artículo científico publicado en 2003

How well does a funneled energy landscape capture the folding mechanism of spectrin domains?

artículo científico publicado en 2013

Hydrophobic core fluidity of homologous protein domains: relation of side-chain dynamics to core composition and packing

artículo científico publicado en 2004

Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin

artículo científico publicado en 2015

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions

scientific article published on 02 April 2019

Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation

artículo científico publicado en 2012

Instrumental Effects in the Dynamics of an Ultrafast Folding Protein under Mechanical Force

scientific article published on 21 August 2018

Locating the Barrier for Folding of Single Molecules under an External Force

scientific article published in Physical Review Letters

Macromolecular crowding effects on protein–protein binding affinity and specificity

artículo científico publicado en 2010

Matching of additive and polarizable force fields for multiscale condensed phase simulations

artículo científico publicado en 2013

Mechanical Unfolding of a Titin Ig Domain: Structure of Transition State Revealed by Combining Atomic Force Microscopy, Protein Engineering and Molecular Dynamics Simulations

artículo científico publicado en 2003

Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering

artículo científico publicado en 2002

Microscopic events in β-hairpin folding from alternative unfolded ensembles

artículo científico publicado en 2011

Microscopic interpretation of folding ϕ-values using the transition path ensemble

artículo científico publicado en 2016

Modest influence of FRET chromophores on the properties of unfolded proteins

artículo científico publicado en 2014

Modulation of Folding Internal Friction by Local and Global Barrier Heights

artículo científico publicado en 2016

Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1α with CBP

scientific article published on 02 September 2011

Molecular Determinants of Aβ Adsorption to Amyloid Fibril Surfaces

article

Molecular origins of internal friction effects on protein-folding rates

artículo científico publicado en 2014

Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes

scientific article published on 19 February 2020

Multiscale simulation reveals multiple pathways for H2 and O2 transport in a [NiFe]-hydrogenase

artículo científico publicado en 2011

Native contacts determine protein folding mechanisms in atomistic simulations

scientific article published on 15 October 2013

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

artículo científico publicado en 2012

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

artículo científico publicado en 2009

Peptide chain dynamics in light and heavy water: zooming in on internal friction

artículo científico publicado en 2012

Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes

artículo científico publicado en 2020

Pressure-induced structural transition of mature HIV-1 protease from a combined NMR/MD simulation approach

artículo científico publicado en 2015

Protein Folding Kinetics Under Force from Molecular Simulation

article

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

artículo científico publicado en 2010

Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules

artículo científico publicado en 2008

Quantitative interpretation of FRET experiments via molecular simulation: force field and validation

artículo científico publicado en 2015

Reaction coordinates and rates from transition paths

artículo científico publicado en 2005

Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion

article

Relation between native ensembles and experimental structures of proteins

artículo científico publicado en 2006

Relation between single-molecule properties and phase behavior of intrinsically disordered proteins

article published in the Proceedings of the National Academy of Sciences of the United States of America

Residue-specific α-helix propensities from molecular simulation

artículo científico publicado en 2012

Role of solvation in pressure-induced helix stabilization ⬇️

artículo científico publicado en 2014

Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations

artículo científico publicado en 2015

Simulation of Coarse-Grained Protein-Protein Interactions with Graphics Processing Units

artículo científico publicado en 2010

Simultaneous determination of protein structure and dynamics.

artículo científico publicado en 2005

Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins

artículo científico publicado en 2011

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

artículo científico publicado en 2009

Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor

article

Smoothing of the GB1 hairpin folding landscape by interfacial confinement

artículo científico publicado en 2012

Structural Interpretation of Hydrogen Exchange Protection Factors in Proteins: Characterization of the Native State Fluctuations of CI2

scientific article published on 01 January 2006

Structural comparison of the two alternative transition states for folding of TI I27.

artículo científico publicado en 2006

Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water

artículo científico publicado en 2010

Temperature-dependent solvation modulates the dimensions of disordered proteins

artículo científico publicado en 2014

The origin of protein sidechain order parameter distributions

artículo científico publicado en 2004

The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding.

artículo científico publicado en 2018

Thermodynamics and kinetics of protein folding under confinement

scholarly article

Transient misfolding dominates multidomain protein folding

artículo científico publicado en 2015

Using Ligand-Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo-Like Kinase 1

artículo científico publicado en 2012

Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data

artículo científico publicado en 2013

What Is the Time Scale for α-Helix Nucleation?

artículo científico publicado en 2011

What can atomic force microscopy tell us about protein folding?

artículo científico publicado en 2002

What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis

artículo científico publicado en 2005

Lista de obras de Robert B. Best

(Ala)(4)-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters

A "slow" protein folds quickly in the end.

A microscopic model for gas diffusion dynamics in a [NiFe]-hydrogenase

A mutant chaperonin with rearranged inter-ring electrostatic contacts and temperature-sensitive dissociation

A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations

A simple method for probing the mechanical unfolding pathway of proteins in detail

A small single-domain protein folds through the same pathway on and off the ribosome

Aerobic damage to [FeFe]-hydrogenases: activation barriers for the chemical attachment of O2.

Are current molecular dynamics force fields too helical?

Atomistic insights into rhodopsin activation from a dynamic model

Atomistic mechanism of transmembrane helix association

Atomistic molecular simulations of protein folding ⬇️

Balance between α and β Structures in Ab Initio Protein Folding

Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association

Binding-induced folding of a natively unstructured transcription factor.

Biochemistry. Unfolding the secrets of calmodulin

Bootstrapping new protein folds

Characterization of the residual structure in the unfolded state of the Δ131Δ fragment of staphylococcal nuclease

Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations

Co-Evolutionary Fitness Landscapes for Sequence Design

Comment on "Force-Clamp Spectroscopy Monitors the Folding Trajectory of a Single Protein"

Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water"

Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations

Complex energy landscape of a giant repeat protein

Computer Folding of RNA Tetraloops? Are We There Yet?

Coordinate-dependent diffusion in protein folding

Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions"

Correction to Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

Correction to Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin

Correction to Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data

Cotranslational folding cooperativity of contiguous domains of α-spectrin

Crosstalk between the protein surface and hydrophobic core in a core-swapped fibronectin type III domain

Cyclic N-terminal loop of amylin forms non amyloid fibers

Dependence of internal friction on folding mechanism

Dependence of protein folding stability and dynamics on the density and composition of macromolecular crowders

Designing an extracellular matrix protein with enhanced mechanical stability

Determination of protein structures consistent with NMR order parameters

Diffusion models of protein folding ⬇️

Diffusive Dynamics of Contact Formation in Disordered Polypeptides ⬇️

Diffusive Model of Protein Folding Dynamics with Kramers Turnover in Rate

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

Disordered RNA chaperones can enhance nucleic acid folding via local charge screening

Effect of interactions with the chaperonin cavity on protein folding and misfolding

Effects of interactions with the GroEL cavity on protein folding rates

Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations

Engineering folding dynamics from two-state to downhill: application to λ-repressor

Evidence for a partially structured state of the amylin monomer

Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties

Exploring the sequence fitness landscape of a bridge between protein folds

Folding Kinetics and Unfolded State Dynamics of the GB1 Hairpin from Molecular Simulation

Folding and binding: when the force is against you.

Folding pathway of an Ig domain is conserved on and off the ribosome

Force-Induced Change in Protein Unfolding Mechanism: Discrete or Continuous Switch?

Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

Hidden complexity in the mechanical properties of titin

How well does a funneled energy landscape capture the folding mechanism of spectrin domains?

Hydrophobic core fluidity of homologous protein domains: relation of side-chain dynamics to core composition and packing

Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions

Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation

Instrumental Effects in the Dynamics of an Ultrafast Folding Protein under Mechanical Force

Locating the Barrier for Folding of Single Molecules under an External Force

Macromolecular crowding effects on protein–protein binding affinity and specificity

Matching of additive and polarizable force fields for multiscale condensed phase simulations

Mechanical Unfolding of a Titin Ig Domain: Structure of Transition State Revealed by Combining Atomic Force Microscopy, Protein Engineering and Molecular Dynamics Simulations

Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering

Microscopic events in β-hairpin folding from alternative unfolded ensembles

Microscopic interpretation of folding ϕ-values using the transition path ensemble

Modest influence of FRET chromophores on the properties of unfolded proteins

Modulation of Folding Internal Friction by Local and Global Barrier Heights

Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1α with CBP

Molecular Determinants of Aβ Adsorption to Amyloid Fibril Surfaces

Molecular origins of internal friction effects on protein-folding rates

Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes

Multiscale simulation reveals multiple pathways for H2 and O2 transport in a [NiFe]-hydrogenase

Native contacts determine protein folding mechanisms in atomistic simulations

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles