List of works - Tobin R. Sosnick

A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable

scientific article published on 23 April 2012

A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations

scientific article published on 23 October 2018

A Probabilistic Graphical Model for Ab Initio Folding

scientific article (publication date: 2009)

A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics

scientific article published on 4 February 2008

A novel implicit solvent model for simulating the molecular dynamics of RNA

scientific article published on September 2013

A probabilistic and continuous model of protein conformational space for template-free modeling

scientific article (publication date: June 2010)

Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics

An adaptive biomolecular condensation response is conserved across environmentally divergent species

scientific article published in 2024

Aromatic claw: A new fold with high aromatic content that evades structural prediction

scientific article

Automated Real-Space Refinement of Protein Structures Using a Realistic Backbone Move Set ⬇️

scientific article published on August 17, 2011

Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding

scholarly article

Benchmarking all-atom simulations using hydrogen exchange

scientific article

Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein–Protein Complexes

scientific article published on 25 February 2022

Characterizing protein folding transition States using Psi-analysis.

scientific article published in January 2007

Characterizing the protein folding transition state using psi analysis

scientific article

Commonly used FRET fluorophores promote collapse of an otherwise disordered protein

scientific article published on 16 April 2019

Commonly-used FRET fluorophores promote collapse of an otherwise disordered protein

Context and Force Field Dependence of the Loss of Protein Backbone Entropy upon Folding Using Realistic Denatured and Native State Ensembles ⬇️

scientific article published on September 14, 2012

Contribution of hydrogen bonding to protein stability estimated from isotope effects

scientific article

Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange

scientific article published on 13 April 2016

D/H amide isotope effect in model alpha-helical peptides

scientific article published in November 2002

De novo prediction of protein folding pathways and structure using the principle of sequential stabilization

scientific article (publication date: 23 October 2012)

Differences in the folding transition state of ubiquitin indicated by phi and psi analyses

scientific article

Discerning the structure and energy of multiple transition states in protein folding using psi-analysis

scientific article

Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface

scientific article (publication date: 30 May 2013)

Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy

scientific article

Distinguishing foldable proteins from nonfolders: when and how do they differ?

scientific article published in October 2002

Early collapse is not an obligate step in protein folding

scientific article published in April 2004

Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization

scientific article published on 21 December 2004

Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion

scientific article

Factors that control the chemistry of the LOV domain photocycle

scientific article published on 27 January 2014

Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding

scientific article published in November 2002

Fast folding of a helical protein initiated by the collision of unstructured chains

scholarly article

Folding of a large protein at high structural resolution

scientific article

Folding of a universal ribozyme: the ribonuclease P RNA.

scientific article published on May 2007

Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures

scholarly article

Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library

scientific article published in July 2005

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.

scientific article published in October 2017

Intramolecular cross-linking evaluated as a structural probe of the protein folding transition state

scientific article published on 7 November 2007

Introduction of a polar core into the de novo designed protein Top7.

scientific article published on 13 February 2016

Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides

scientific article

Investigations of human myosin VI targeting using optogenetically controlled cargo loading

scientific article published on 13 February 2017

Kinetic barriers and the role of topology in protein and RNA folding

scientific article published on 23 May 2008

Large-scale context in protein folding: villin headpiece

scientific article published on January 2003

Light-activated DNA binding in a designed allosteric protein

scholarly article

Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations

scientific article

Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates

scientific article published on April 2009

Methods for the accurate estimation of confidence intervals on protein folding phi-values

scientific article

Mimicking the folding pathway to improve homology-free protein structure prediction.

scientific article

Minimalist representations and the importance of nearest neighbor effects in protein folding simulations

scientific article

Modeling large regions in proteins: Applications to loops, termini, and folding ⬇️

scientific article published on December 5, 2011

Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering ⬇️

scientific article published on October 19, 2011

Modeling the hydration layer around proteins: HyPred

scientific article

New era of molecular structure and dynamics from solution scattering experiments ⬇️

scientific article published on August 1, 2011

On docking, scoring and assessing protein-DNA complexes in a rigid-body framework

scientific article

On the precision of experimentally determined protein folding rates and phi-values

scientific article

Outcome of a workshop on applications of protein models in biomedical research

scientific article (publication date: 13 February 2009)

PII structure in the model peptides for unfolded proteins: studies on ubiquitin fragments and several alanine-rich peptides containing QQQ, SSS, FFF, and VVV.

scientific article published in May 2006

Prediction and Validation of a Protein’s Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence

scientific article published on 22 December 2021

Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions

scholarly article

Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding

scientific article published in December 2008

Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

scientific article published on 02 September 2020

Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins

scientific article

Protein structure prediction enhanced with evolutionary diversity: SPEED.

scientific article

Protein vivisection reveals elusive intermediates in folding

scientific article

Psi-constrained simulations of protein folding transition states: implications for calculating

scientific article published on March 2009

Quantifying the structural requirements of the folding transition state of protein A and other systems

scientific article published on July 2008

RNA folding during transcription

scientific article

RNA folding: models and perspectives

scientific article

Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions

scientific article published on 11 May 2015

Random-coil behavior and the dimensions of chemically unfolded proteins

scholarly article

Rationally improving LOV domain-based photoswitches

scientific article published on 20 June 2010

Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification

scientific article

Response to Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

scientific article published in Science

Revealing what gets buried first in protein folding

scientific article published on 04 October 2013

Simplified protein models: predicting folding pathways and structure using amino acid sequences

scientific article published on 11 July 2013

Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA.

scholarly article

Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme

scientific article published on 2 January 2004

Small-Angle X-ray Scattering and Single-Molecule FRET Spectroscopy Produce Highly Divergent Views of the Low-Denaturant Unfolded State ⬇️

scientific article published on January 27, 2012

Statistical coil model of the unfolded state: resolving the reconciliation problem

scientific article published on 30 August 2005

Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response

scientific article published in March 2017

Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium

scientific article published in April 2006

TULIPs: tunable, light-controlled interacting protein tags for cell biology ⬇️

scientific article published on March 4, 2012

The Amino-Terminal Helix Modulates Light-Activated Conformational Changes in AsLOV2 ⬇️

scientific article published on March 7, 2012

The Folding Transition State of Protein L Is Extensive with Nonnative Interactions (and Not Small and Polarized) ⬇️

scientific article published on April 18, 2012

The Highly Cooperative Folding of Small Naturally Occurring Proteins Is Likely the Result of Natural Selection

article by Alexander L. Watters et al published February 2007 in Cell

The Pentablock Amphiphilic Copolymer T1107 Prevents Aggregation of Denatured and Reduced Lysozyme

scientific article published on 12 September 2016

The folding of single domain proteins—have we reached a consensus? ⬇️

scientific article published on 06 December 2010

Thymosin beta 4 binds actin in an extended conformation and contacts both the barbed and pointed ends

scientific article (publication date: 13 May 1997)

Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours

scientific article published on 27 December 2018

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch ⬇️

scientific article published on February 13, 2012

Ubiquitin is a novel substrate for human insulin-degrading enzyme

scientific article

Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects

scientific article

List of works by Tobin R. Sosnick

A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable

A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations

A Probabilistic Graphical Model for Ab Initio Folding

A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics

A novel implicit solvent model for simulating the molecular dynamics of RNA

A probabilistic and continuous model of protein conformational space for template-free modeling

Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics

An adaptive biomolecular condensation response is conserved across environmentally divergent species

Aromatic claw: A new fold with high aromatic content that evades structural prediction

Automated Real-Space Refinement of Protein Structures Using a Realistic Backbone Move Set ⬇️

Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding

Benchmarking all-atom simulations using hydrogen exchange

Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein–Protein Complexes

Characterizing protein folding transition States using Psi-analysis.

Characterizing the protein folding transition state using psi analysis

Commonly used FRET fluorophores promote collapse of an otherwise disordered protein

Commonly-used FRET fluorophores promote collapse of an otherwise disordered protein

Context and Force Field Dependence of the Loss of Protein Backbone Entropy upon Folding Using Realistic Denatured and Native State Ensembles ⬇️

Contribution of hydrogen bonding to protein stability estimated from isotope effects

Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange

D/H amide isotope effect in model alpha-helical peptides

De novo prediction of protein folding pathways and structure using the principle of sequential stabilization

Differences in the folding transition state of ubiquitin indicated by phi and psi analyses

Discerning the structure and energy of multiple transition states in protein folding using psi-analysis

Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface

Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy

Distinguishing foldable proteins from nonfolders: when and how do they differ?

Early collapse is not an obligate step in protein folding

Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization

Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion

Factors that control the chemistry of the LOV domain photocycle

Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding

Fast folding of a helical protein initiated by the collision of unstructured chains

Folding of a large protein at high structural resolution

Folding of a universal ribozyme: the ribonuclease P RNA.

Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures

Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.

Intramolecular cross-linking evaluated as a structural probe of the protein folding transition state

Introduction of a polar core into the de novo designed protein Top7.

Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides

Investigations of human myosin VI targeting using optogenetically controlled cargo loading

Kinetic barriers and the role of topology in protein and RNA folding

Large-scale context in protein folding: villin headpiece

Light-activated DNA binding in a designed allosteric protein

Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations

Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates

Methods for the accurate estimation of confidence intervals on protein folding phi-values

Mimicking the folding pathway to improve homology-free protein structure prediction.

Minimalist representations and the importance of nearest neighbor effects in protein folding simulations

Modeling large regions in proteins: Applications to loops, termini, and folding ⬇️

Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering ⬇️

Modeling the hydration layer around proteins: HyPred

New era of molecular structure and dynamics from solution scattering experiments ⬇️

On docking, scoring and assessing protein-DNA complexes in a rigid-body framework

On the precision of experimentally determined protein folding rates and phi-values

Outcome of a workshop on applications of protein models in biomedical research

PII structure in the model peptides for unfolded proteins: studies on ubiquitin fragments and several alanine-rich peptides containing QQQ, SSS, FFF, and VVV.

Prediction and Validation of a Protein’s Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence

Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions

Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding

Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins

Protein structure prediction enhanced with evolutionary diversity: SPEED.

Protein vivisection reveals elusive intermediates in folding

Psi-constrained simulations of protein folding transition states: implications for calculating

Quantifying the structural requirements of the folding transition state of protein A and other systems

RNA folding during transcription

RNA folding: models and perspectives

Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions

Random-coil behavior and the dimensions of chemically unfolded proteins

Rationally improving LOV domain-based photoswitches

Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification

Response to Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

Revealing what gets buried first in protein folding

Simplified protein models: predicting folding pathways and structure using amino acid sequences

Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA.

Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme

Small-Angle X-ray Scattering and Single-Molecule FRET Spectroscopy Produce Highly Divergent Views of the Low-Denaturant Unfolded State ⬇️