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List of works by Tongye Shen

A coarse-grained model for synergistic action of multiple enzymes on cellulose

scientific article

A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw

scholarly article

A statistical analysis of the precision of reweighting-based simulations

scientific article published on 01 July 2008

Appreciating HIV type 1 diversity: subtype differences in Env.

scientific article

Brownian dynamics simulation of helix-capping motifs.

scientific article

Brownian dynamics simulation of peptides with the University of Houston Brownian Dynamics (UHBD) program

scientific article

CAMERRA: An analysis tool for the computation of conformational dynamics by evaluating residue-residue associations

scientific article published on 21 February 2018

Changes in flexibility upon binding: Application of the self-consistent pair contact probability method to protein-protein interactions

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

scientific article published in January 2018

Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework

scientific article published on 01 September 2018

Conformational flexibility of soluble cellulose oligomers: chain length and temperature dependence

scientific article published in October 2009

Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles.

scientific article published on 17 January 2008

DMSO enhanced conformational switch of an interfacial enzyme

scientific article published on 27 July 2016

Effector-Binding-Directed Dimerization and Dynamic Communication between Allosteric Sites of Ribonucleotide Reductase

scientific article published on 08 January 2019

Effects of Branched O-Glycosylation on a Semiflexible Peptide Linker

scientific article published on 18 February 2014

Elasticity of peptide omega bonds

scientific article published on 10 April 2006

Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin

scholarly article

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model

scientific article

High-pressure effect on the dynamics of solvated peptides

scientific article published on 01 April 2012

In silico studies of crystalline cellulose and its degradation by enzymes

scientific article

Insight into the role of hydration on protein dynamics.

scientific article published in September 2006

Investigation of Carbohydrate Recognition via Computer Simulation

scientific article

Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts

scientific article published on 06 February 2015

Molecular dynamics of acetylcholinesterase

scientific article (publication date: June 2002)

Nonequilibrium self-assembly of linear fibers: microscopic treatment of growth, decay, catastrophe and rescue

scientific article published on 31 March 2006

Nonequilibrium statistical mechanical models for cytoskeletal assembly: towards understanding tensegrity in cells

scientific article

Nucleation dynamics of active particles

scientific article published on 2 July 2013

Phenotypic variability of growing cellular populations

scholarly article

Phi-value analysis of apo-azurin folding: comparison between experiment and theory

scientific article published in May 2006

Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis

scientific article published in February 2005

Pressure-induced conformational switch of an interfacial protein

scientific article published on 16 April 2016

Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections

scientific article

Regulatory Mechanics of Constitutive Androstane Receptors: Basal and Ligand-Directed Actions

scientific article published on 02 December 2019

Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations.

scientific article published in June 2005

Scanning malleable transition state ensembles: comparing theory and experiment for folding protein U1A.

scientific article published in May 2005

Solvent-dependent gating motions of an extremophilic lipase from Pseudomonas aeruginosa

scientific article published in 2012

Solvent-induced α- to 3(10)-helix transition of an amphiphilic peptide

scientific article published on 25 September 2013

Stability and Sugar Recognition Ability of Ricin-like Carbohydrate Binding Domains

scientific article published on 21 April 2011

Stability and dynamics of crystals and glasses of motorized particles

scholarly article

Subtype-specific conservation of isoleucine 309 in the envelope V3 domain is linked to immune evasion in subtype C HIV-1 infection

scientific article published on 21 May 2010

Swimming motility plays a key role in the stochastic dynamics of cell clumping

scientific article published on 18 February 2013

Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery

scientific article

The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor

scientific article published on 25 April 2016

The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain

scientific article published in September 2005

The interplay of nonlinearity and architecture in equilibrium cytoskeletal mechanics.

scientific article published in January 2011

The stability of cellulose: a statistical perspective from a coarse-grained model of hydrogen-bond networks

scientific article (publication date: 22 April 2009)

Transfer matrix approach to the hydrogen-bonding in cellulose Iα fibrils describes the recalcitrance to thermal deconstruction

scientific article published on 01 August 2011

Unfolding proteins under external forces: a solvable model under the self-consistent pair contact probability approximation

scientific article published on 22 July 2002

Using contact statistics to characterize structure transformation of biopolymer ensembles

scientific article published on 01 January 2020

Variationally determined free energy profiles for structural models of proteins: characteristic temperatures for folding and trapping

scientific article published in April 2008

Water’s Contribution to the Energetic Roughness from Peptide Dynamics

scientific article published on 01 September 2010

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