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References from Osmolyte-induced protein stability changes explained by graph theory. Local targets link to admitted publications; unresolved targets remain external evidence.
Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
10.1039/c7cp07436k · 2018 · External reference
Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis
10.1038/s41598-020-66710-6 · 2020 · External reference
The stabilization of proteins by osmolytes
10.1016/s0006-3495(85)83932-1 · 1985 · External reference
Anatomy of energetic changes accompanying urea-induced protein denaturation
10.1073/pnas.0706251104 · 2007 · External reference
The Protein Data Bank
10.1093/nar/28.1.235 · 2000 · External reference
10.1021/acsomega.8b01911
10.1021/acsomega.8b01911 · External reference
10.1146/annurev.biochem.77.061306.131357
10.1146/annurev.biochem.77.061306.131357 · External reference
A network representation of protein structures: implications for protein stability
10.1529/biophysj.105.064485 · 2005 · External reference
The biomolecular simulation program
10.1002/jcc.21287 · 2009 · External reference
Canonical sampling through velocity-rescaling
2007 · External reference
10.1146/annurev-physchem-040412-110156
10.1146/annurev-physchem-040412-110156 · External reference
Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins
10.1021/ja00119a045 · 1995 · External reference
Spatial organization of hydrophobic and charged residues affects protein thermal stability and binding affinity
2022 · External reference
10.1073/pnas.1718910115
10.1073/pnas.1718910115 · External reference
Simulation of urea-induced protein unfolding: a lesson from bovine β-lactoglobulin
10.1016/j.jmgm.2011.06.004 · 2011 · External reference
Classification of conformational stability of protein mutants from 3D pseudo-folding graph representation of protein sequences using support vector machines
10.1002/prot.21524 · 2008 · External reference
10.1039/c5ra08612d
10.1039/c5ra08612d · External reference
Trimethylamine n-oxide counteracts urea denaturation by inhibiting protein–urea preferential interaction
10.1021/jacs.7b11695 · 2017 · External reference
Mechanism of protein stabilization by glycerol: preferential hydration in glycerol-water mixtures
10.1021/bi00519a023 · 1981 · External reference
NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation
10.1186/1471-2164-15-s4-s7 · 2014 · External reference
Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer
10.1073/pnas.1109372108 · 2011 · External reference
10.1016/s0091-679x(07)84022-2
10.1016/s0091-679x(07)84022-2 · External reference
LINCS: a linear constraint solver for molecular simulations
10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.0.co;2-h · 1997 · External reference
10.1063/1.445869
10.1063/1.445869 · External reference
10.1016/j.csbj.2023.09.016 · Admitted local publication
10.1016/j.addr.2011.07.006
10.1016/j.addr.2011.07.006 · External reference
10.1002/iub.406
10.1002/iub.406 · External reference
The hydrogen bond network structure within the hydration shell around simple osmolytes: urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
2010 · External reference
10.1021/acs.jpcb.5b08029
10.1021/acs.jpcb.5b08029 · External reference
10.1039/c5py00121h
10.1039/c5py00121h · External reference
How do trehalose, maltose, and sucrose influence some structural and dynamical properties of lysozyme? Insight from molecular dynamics simulations
10.1021/jp071946z · 2007 · External reference
Why do some organisms use a urea-methylamine mixture as osmolyte? Thermodynamic compensation of urea and trimethylamine N-oxide interactions with protein
10.1021/bi00208a021 · 1994 · External reference
10.1002/prot.10632
10.1002/prot.10632 · External reference
Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations
2010 · External reference
10.3390/biom10121664
10.3390/biom10121664 · External reference
Effects of osmolytes on the helical conformation of model peptide: molecular dynamics simulation
2011 · External reference
Thermometer: a webserver to predict protein thermal stability
10.1093/bioinformatics/btab868 · 2022 · External reference
10.1093/bioinformatics/bty1011
10.1093/bioinformatics/bty1011 · External reference
Simulated epidemics in 3d protein structures to detect functional properties
10.1021/acs.jcim.9b01027 · 2020 · External reference
10.1016/j.addr.2011.06.011
10.1016/j.addr.2011.06.011 · External reference
Crystal structure and pair potentials: a molecular-dynamics study
10.1103/physrevlett.45.1196 · 1980 · External reference
Effect of sorbitol and glycerol on the stability of trypsin and difference between their stabilization effects in the various solvents
10.1002/bab.1366 · 2016 · External reference
Blundell. mCSM: predicting the effects of mutations in proteins using graph-based signatures
10.1093/bioinformatics/btt691 · 2014 · External reference
10.1021/jacs.8b03903
10.1021/jacs.8b03903 · External reference
Molecular aggregation behavior and microscopic heterogeneity in binary osmolyte–water solutions
2023 · External reference
Molecular computations of preferential interaction coefficients of proteins
10.1021/jp810949t · 2009 · External reference
10.1039/c6cp07903b
10.1039/c6cp07903b · External reference
10.1016/s0301-4622(03)00095-4
10.1016/s0301-4622(03)00095-4 · External reference
10.1021/acs.jcim.1c00527
10.1021/acs.jcim.1c00527 · External reference
Control of protein stability and reactions by weakly interacting cosolvents: the simplicity of the complicated
10.1016/s0065-3233(08)60656-7 · 1998 · External reference
Water as ligand: preferential binding and exclusion of denaturants in protein unfolding
10.1021/bi00156a001 · 1992 · External reference
Protein hydration, thermodynamic binding, and preferential hydration
10.1021/bi020316e · 2002 · External reference
10.1073/pnas.122225399
10.1073/pnas.122225399 · External reference
10.1002/jcc.20291
10.1002/jcc.20291 · External reference
10.1142/s0219633602000117
10.1142/s0219633602000117 · External reference
Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networks
10.1039/c9cp03009c · 2019 · External reference
10.1002/jcc.21816
10.1002/jcc.21816 · External reference
