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List of works by 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

scientific article published on 29 November 2012

A "slow" protein folds quickly in the end.

scientific article published on April 2013

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

scientific article published on 14 March 2011

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

scientific article

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

scientific article

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

scientific article

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.

scientific article

Are current molecular dynamics force fields too helical?

scientific article

Atomistic insights into rhodopsin activation from a dynamic model

scientific article published on 12 July 2008

Atomistic mechanism of transmembrane helix association

scientific article published on 04 June 2020

Atomistic molecular simulations of protein folding ⬇️

scientific article published on January 17, 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

scientific article

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

scientific article published on 9 February 2018

Binding-induced folding of a natively unstructured transcription factor.

scientific article

Biochemistry. Unfolding the secrets of calmodulin

scientific article published on January 2009

Bootstrapping new protein folds

scientific article

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

scholarly article

Co-Evolutionary Fitness Landscapes for Sequence Design

article

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

scientific article published in Science

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

scientific article published on 15 October 2013

Complex energy landscape of a giant repeat protein

scientific article

Computer Folding of RNA Tetraloops? Are We There Yet?

scientific article published on 7 March 2013

Coordinate-dependent diffusion in protein folding

scientific article

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

scientific article published on April 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

scientific article

Cotranslational folding cooperativity of contiguous domains of α-spectrin

scientific article published on 08 June 2020

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

scientific article published on 25 October 2007

Cyclic N-terminal loop of amylin forms non amyloid fibers

scientific article published on October 2013

Dependence of internal friction on folding mechanism

scientific article

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

scientific article

Designing an extracellular matrix protein with enhanced mechanical stability

scientific article

Determination of protein structures consistent with NMR order parameters

scientific article published in July 2004

Diffusion models of protein folding ⬇️

scientific article published on August 15, 2011

Diffusive Dynamics of Contact Formation in Disordered Polypeptides ⬇️

scientific article published on 11 February 2016

Diffusive Model of Protein Folding Dynamics with Kramers Turnover in Rate

scientific article published in Physical Review Letters

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

scientific article

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

scientific article published on 05 June 2019

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

scientific article

Effects of interactions with the GroEL cavity on protein folding rates

scientific article published on March 2013

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

scientific article published on 13 October 2015

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

scientific article published on 22 October 2013

Evidence for a partially structured state of the amylin monomer

scientific article published on December 2009

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

scientific article published on 22 April 2019

Exploring the sequence fitness landscape of a bridge between protein folds

scientific article published on 13 October 2020

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

scientific article published on 7 February 2013

Folding and binding: when the force is against you.

scientific article published on December 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

scientific article published on April 2012

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

scientific article

Hidden complexity in the mechanical properties of titin

scientific article published in Nature

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

scientific article

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

scientific article published in February 2004

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

scientific article published on 01 April 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

scientific article

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

scientific article published on 01 November 2010

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

scientific article published on June 2013

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

scientific article published on 01 July 2003

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

scientific article (publication date: 27 September 2002)

Microscopic events in β-hairpin folding from alternative unfolded ensembles

scientific article

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

scientific article published on 8 March 2016

Modest influence of FRET chromophores on the properties of unfolded proteins

scientific article

Modulation of Folding Internal Friction by Local and Global Barrier Heights

scientific article published on 7 March 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

scientific article

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

scientific article published on 22 February 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

scientific article published on 18 July 2012

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

scientific article

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

scientific article published on 27 March 2012

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

scientific article published on 12 November 2020

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

scientific article

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

scientific article published on 01 November 2010

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

scientific article published on 6 February 2008

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

scientific article published on June 2015

Reaction coordinates and rates from transition paths

scientific article

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

article

Relation between native ensembles and experimental structures of proteins

scholarly article

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

scientific article published on 20 March 2012

Role of solvation in pressure-induced helix stabilization ⬇️

scientific article

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

scientific article published on 26 October 2015

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

scientific article

Simultaneous determination of protein structure and dynamics.

scientific article

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

scientific article

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

scholarly article

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

scientific article

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.

scientific article

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

scientific article

Temperature-dependent solvation modulates the dimensions of disordered proteins

scientific article published on 21 March 2014

The origin of protein sidechain order parameter distributions

scientific article

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

scientific article published on 26 November 2018

Thermodynamics and kinetics of protein folding under confinement

scholarly article

Transient misfolding dominates multidomain protein folding

scientific article

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

scientific article

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

scientific article

What Is the Time Scale for α-Helix Nucleation?

scientific article published on 11 April 2011

What can atomic force microscopy tell us about protein folding?

scientific article published on 01 February 2002

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

scientific article

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