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  4. Robert B. Best, Ph.D.
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Robert B. Best, Ph.D.
Robert Best.
Section Chief: Computational Biophysics Section, Laboratory of Chemical Physics
Scientific Focus Areas: Biomedical Engineering and Biophysics, Computational Biology, Structural Biology

Publications

A selection of recent and significant publications can be viewed below.

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On the role of native contact cooperativity in protein folding.
Wang D, Frechette LB, Best RB.
Proc Natl Acad Sci U S A (2024 May 28) 121:e2319249121. Abstract/Full Text
Extreme dynamics in a biomolecular condensate.
Galvanetto N, Ivanović MT, Chowdhury A, Sottini A, Nüesch MF, Nettels D, Best RB, Schuler B.
Nature (2023 Jul) 619:876-883. Abstract/Full Text
A Data-Driven Hydrophobicity Scale for Predicting Liquid-Liquid Phase Separation of Proteins.
Dannenhoffer-Lafage T, Best RB.
J Phys Chem B (2021 Apr 29) 125:4046-4056. Abstract/Full Text
Co-Evolutionary Fitness Landscapes for Sequence Design.
Tian P, Louis JM, Baber JL, Aniana A, Best RB.
Angew Chem Int Ed Engl (2018 May 14) 57:5674-5678. Abstract/Full Text
Folding pathway of an Ig domain is conserved on and off the ribosome.
Tian P, Steward A, Kudva R, Su T, Shilling PJ, Nickson AA, Hollins JJ, Beckmann R, von Heijne G, Clarke J, Best RB.
Proc Natl Acad Sci U S A (2018 Nov 27) 115:E11284-E11293. Abstract/Full Text

Additional Publications

Instrumental Effects in the Dynamics of an Ultrafast Folding Protein under Mechanical Force.
De Sancho D, Schönfelder J, Best RB, Perez-Jimenez R, Muñoz V.
J Phys Chem B (2018 Dec 13) 122:11147-11154. Abstract/Full Text
An Extended Guinier Analysis for Intrinsically Disordered Proteins.
Zheng W, Best RB.
J Mol Biol (2018 Aug 3) 430:2540-2553. Abstract/Full Text
Inferring properties of disordered chains from FRET transfer efficiencies.
Zheng W, Zerze GH, Borgia A, Mittal J, Schuler B, Best RB.
J Chem Phys (2018 Mar 28) 148:123329. Abstract/Full Text
Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation.
Meng F, Bellaiche MMJ, Kim JY, Zerze GH, Best RB, Chung HS.
Biophys J (2018 Feb 27) 114:870-884. Abstract/Full Text
Sequence determinants of protein phase behavior from a coarse-grained model.
Dignon GL, Zheng W, Kim YC, Best RB, Mittal J.
PLoS Comput Biol (2018 Jan) 14:e1005941. Abstract/Full Text
How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis.
Tian P, Best RB.
Biophys J (2017 Oct 17) 113:1719-1730. Abstract/Full Text
Phosphorylation of the FUS low-complexity domain disrupts phase separation, aggregation, and toxicity.
Monahan Z, Ryan VH, Janke AM, Burke KA, Rhoads SN, Zerze GH, O'Meally R, Dignon GL, Conicella AE, Zheng W, Best RB, Cole RN, Mittal J, Shewmaker F, Fawzi NL.
EMBO J (2017 Oct 16) 36:2951-2967. Abstract/Full Text
Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association.
Domański J, Hedger G, Best RB, Stansfeld PJ, Sansom MSP.
J Phys Chem B (2017 Apr 20) 121:3364-3375. Abstract/Full Text
Computational and theoretical advances in studies of intrinsically disordered proteins.
Best RB.
Curr Opin Struct Biol (2017 Feb) 42:147-154. Abstract/Full Text
Mechanism of O(2) diffusion and reduction in FeFe hydrogenases.
Kubas A, Orain C, De Sancho D, Saujet L, Sensi M, Gauquelin C, Meynial-Salles I, Soucaille P, Bottin H, Baffert C, Fourmond V, Best RB, Blumberger J, Léger C.
Nat Chem (2017 Jan) 9:88-95. Abstract/Full Text
Reconciling Intermediates in Mechanical Unfolding Experiments with Two-State Protein Folding in Bulk.
de Sancho D, Best RB.
J Phys Chem Lett (2016 Oct 6) 7:3798-3803. Abstract/Full Text
Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.
Borgia A, Zheng W, Buholzer K, Borgia MB, Schüler A, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A, Best RB, Schuler B.
J Am Chem Soc (2016 Sep 14) 138:11714-26. Abstract/Full Text
Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment.
Zheng W, Borgia A, Buholzer K, Grishaev A, Schuler B, Best RB.
J Am Chem Soc (2016 Sep 14) 138:11702-13. Abstract/Full Text
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.
Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P.
J Chem Theory Comput (2016 Sep 13) 12:4534-48. Abstract/Full Text
Structural Determinants of Misfolding in Multidomain Proteins.
Tian P, Best RB.
PLoS Comput Biol (2016 May) 12:e1004933. Abstract/Full Text
Modulation of Folding Internal Friction by Local and Global Barrier Heights.
Zheng W, de Sancho D, Best RB.
J Phys Chem Lett (2016 Mar 17) 7:1028-34. Abstract/Full Text
Markov state models of protein misfolding.
Sirur A, De Sancho D, Best RB.
J Chem Phys (2016 Feb 21) 144:075101. Abstract/Full Text
Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion.
Zheng W, Best RB.
J Phys Chem B (2015 Dec 10) 119:15247-55. Abstract/Full Text
Pressure-induced structural transition of mature HIV-1 protease from a combined NMR/MD simulation approach.
Roche J, Louis JM, Bax A, Best RB.
Proteins (2015 Dec) 83:2117-23. Abstract/Full Text
Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations.
Zerze GH, Best RB, Mittal J.
J Phys Chem B (2015 Nov 19) 119:14622-30. Abstract/Full Text
Transient misfolding dominates multidomain protein folding.
Borgia A, Kemplen KR, Borgia MB, Soranno A, Shammas S, Wunderlich B, Nettels D, Best RB, Clarke J, Schuler B.
Nat Commun (2015 Nov 17) 6:8861. Abstract/Full Text
Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations.
Zheng W, Borgia A, Borgia MB, Schuler B, Best RB.
J Chem Theory Comput (2015 Nov 10) 11:5543-53. Abstract/Full Text
Quantitative interpretation of FRET experiments via molecular simulation: force field and validation.
Best RB, Hofmann H, Nettels D, Schuler B.
Biophys J (2015 Jun 2) 108:2721-31. Abstract/Full Text
Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin.
De Sancho D, Kubas A, Wang PH, Blumberger J, Best RB.
J Chem Theory Comput (2015 Apr 14) 11:1919-27. Abstract/Full Text
Dependence of internal friction on folding mechanism.
Zheng W, De Sancho D, Hoppe T, Best RB.
J Am Chem Soc (2015 Mar 11) 137:3283-90. Abstract/Full Text
Role of solvation in pressure-induced helix stabilization.
Best RB, Miller C, Mittal J.
J Chem Phys (2014 Dec 14) 141:22D522. Abstract/Full Text
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association.
Best RB, Zheng W, Mittal J.
J Chem Theory Comput (2014 Nov 11) 10:5113-5124. Abstract/Full Text
Modest influence of FRET chromophores on the properties of unfolded proteins.
Zerze GH, Best RB, Mittal J.
Biophys J (2014 Oct 7) 107:1654-60. Abstract/Full Text
Bootstrapping new protein folds.
Best RB.
Biophys J (2014 Sep 2) 107:1040-1041. Abstract/Full Text
Molecular origins of internal friction effects on protein-folding rates.
de Sancho D, Sirur A, Best RB.
Nat Commun (2014 Jul 2) 5:4307. Abstract/Full Text
Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model.
Knott M, Best RB.
J Chem Phys (2014 May 7) 140:175102. Abstract/Full Text
Effect of interactions with the chaperonin cavity on protein folding and misfolding.
Sirur A, Knott M, Best RB.
Phys Chem Chem Phys (2014 Apr 14) 16:6358-66. Abstract/Full Text
Aerobic damage to [FeFe]-hydrogenases: activation barriers for the chemical attachment of O2.
Kubas A, De Sancho D, Best RB, Blumberger J.
Angew Chem Int Ed Engl (2014 Apr 14) 53:4081-4. Abstract/Full Text
Temperature-dependent solvation modulates the dimensions of disordered proteins.
Wuttke R, Hofmann H, Nettels D, Borgia MB, Mittal J, Best RB, Schuler B.
Proc Natl Acad Sci U S A (2014 Apr 8) 111:5213-8. Abstract/Full Text
Folding and binding: when the force is against you.
Best RB.
Biophys J (2013 Dec 17) 105:2611-2. Abstract/Full Text
Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.
Bottaro S, Lindorff-Larsen K, Best RB.
J Chem Theory Comput (2013 Dec 10) 9:5641-5652. Abstract/Full Text
Engineering folding dynamics from two-state to downhill: application to λ-repressor.
Carter JW, Baker CM, Best RB, De Sancho D.
J Phys Chem B (2013 Oct 31) 117:13435-43. Abstract/Full Text
Native contacts determine protein folding mechanisms in atomistic simulations.
Best RB, Hummer G, Eaton WA.
Proc Natl Acad Sci U S A (2013 Oct 29) 110:17874-9. Abstract/Full Text
Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.
Henry ER, Best RB, Eaton WA.
Proc Natl Acad Sci U S A (2013 Oct 29) 110:17880-5. Abstract/Full Text
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.
Shi Y, Xia Z, Zhang J, Best R, Wu C, Ponder JW, Ren P.
J Chem Theory Comput (2013) 9:4046-4063. Abstract/Full Text
Last Reviewed April 2025