Lista de obras - Tobin Roy Sosnick - Dominio Público Uruguay

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

artículo científico publicado en 2012

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

artículo científico publicado en 2018

A Probabilistic Graphical Model for Ab Initio Folding ⬇️

artículo científico publicado el 1 de enero de 2009

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2024

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

artículo científico publicado en 2016

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

artículo científico publicado el 17 de agosto de 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

artículo científico publicado en 2014

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

artículo científico publicado en 2022

Characterizing protein folding transition States using Psi-analysis.

artículo científico publicado en 2007

Characterizing the protein folding transition state using psi analysis

artículo científico publicado en 2006

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 ⬇️

artículo científico publicado el 14 de septiembre de 2012

Contribution of hydrogen bonding to protein stability estimated from isotope effects

artículo científico publicado en 2002

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

artículo científico publicado en 2016

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

artículo científico publicado en 2002

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

artículo científico publicado el 8 de octubre de 2012

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

artículo científico publicado en 2004

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

artículo científico publicado en 2004

Discovering RNA-Protein Interactome by Using Chemical Context Profiling of the RNA-Protein Interface ⬇️

artículo científico publicado el 9 de mayo de 2013

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

artículo científico publicado en 2010

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

artículo científico publicado en 2002

Early collapse is not an obligate step in protein folding

artículo científico publicado en 2004

Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization

artículo científico publicado en 2004

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

artículo científico publicado en 2010

Factors that control the chemistry of the LOV domain photocycle

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2013

Folding of a universal ribozyme: the ribonuclease P RNA.

artículo científico publicado en 2007

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

artículo científico publicado en 2007

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

artículo científico publicado en 2005

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

artículo científico publicado en 2017

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

artículo científico publicado en 2007

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

artículo científico publicado en 2016

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

artículo científico publicado en 2003

Investigations of human myosin VI targeting using optogenetically controlled cargo loading

artículo científico publicado en 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

artículo científico publicado en 2003

Light-activated DNA binding in a designed allosteric protein

artículo científico publicado en 2008

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

artículo científico publicado en 2014

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

artículo científico publicado en 2009

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

artículo científico publicado en 2006

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

artículo científico publicado en 2009

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

artículo científico publicado en 2006

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

artículo científico publicado el 5 de diciembre de 2011

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

artículo científico publicado el 19 de octubre de 2011

Modeling the hydration layer around proteins: HyPred

artículo científico publicado en 2010

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

artículo científico publicado el 1 de agosto de 2011

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

artículo científico publicado en 2012

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

artículo científico publicado en 2006

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

artículo científico publicado en 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.

artículo científico publicado en 2006

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

artículo científico publicado en 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

artículo científico publicado en 2008

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

artículo científico publicado en 2020

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

artículo científico publicado en 2005

Protein structure prediction enhanced with evolutionary diversity: SPEED.

artículo científico publicado en 2010

Protein vivisection reveals elusive intermediates in folding

artículo científico publicado en 2010

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

artículo científico publicado en 2009

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

artículo científico publicado en 2008

RNA folding during transcription

artículo científico publicado en 2006

RNA folding: models and perspectives

artículo científico publicado en 2003

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

artículo científico publicado en 2015

Random-coil behavior and the dimensions of chemically unfolded proteins

scholarly article

Rationally improving LOV domain-based photoswitches

artículo científico publicado en 2010

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

artículo científico publicado en 2007

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

artículo científico publicado en 2018

Revealing what gets buried first in protein folding

artículo científico publicado en 2013

Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences ⬇️

artículo científico publicado el 11 de julio de 2013

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

artículo científico publicado en 2008

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

artículo científico publicado en 2004

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

artículo científico publicado el 27 de enero de 2012

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

artículo científico publicado en 2005

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

artículo científico publicado en 2017

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

artículo científico publicado en 2006

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

artículo científico publicado el 4 de marzo de 2012

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

artículo científico publicado el 7 de marzo de 2012

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

artículo científico publicado el 18 de abril de 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

artículo científico publicado en 2016

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

artículo científico publicado el 6 de diciembre de 2010

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

artículo científico publicado en 1997

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

artículo científico publicado en 2018

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

artículo científico publicado el 13 de febrero de 2012

Ubiquitin is a novel substrate for human insulin-degrading enzyme

artículo científico publicado en 2011

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

artículo científico publicado en 2002

Lista de obras de Tobin Roy 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 ⬇️