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Towards a structural biology of the hydrophobic effect in protein folding
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Protein Folding: A Perspective from Theory and Experiment
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Cold Denaturation Unveiled: Molecular Mechanism of the Asymmetric Unfolding of Yeast Frataxin
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ALMOST: An all atom molecular simulation toolkit for protein structure determination
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Protein folding dynamics: The diffusion‐collision model and experimental data
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Funnels, pathways, and the energy landscape of protein folding: A synthesis
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Structure in Aqueous Solutions of Nonpolar Solutes from the Standpoint of Scaled-Particle Theory
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Structure in aqueous solutions of nonpolar solutes from the standpoint of scaled-particle theory
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The folding of an enzyme
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PLUMED 2: New feathers for an old bird
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The Role of Hydration in Protein Stability: Comparison of the Cold and Heat Unfolded States of Yfh1
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Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
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Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins
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Energetics of Protein Structure
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Water Mediated Interactions and the Protein Folding Phase Diagram in the Temperature–Pressure Plane
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Water as an Active Constituent in Cell Biology
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On the Use of Experimental Observations to Bias Simulated Ensembles
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P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
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A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1
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Unbiased Cold Denaturation: Low- and High-Temperature Unfolding of Yeast Frataxin under Physiological Conditions
inferredcites →https://doi.org/10.1021/ja407009wopenalex-snapshot
Single-Molecule Spectroscopy of Cold Denaturation and the Temperature-Induced Collapse of Unfolded Proteins
inferredcites →https://doi.org/10.1021/ja5027584openalex-snapshot
Statistical Mechanics of the Denatured State of a Protein Using Replica-Averaged Metadynamics
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Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances
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A Bias-Exchange Approach to Protein Folding
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Mechanistic Elements of Protein Cold Denaturation
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Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse
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Hydrophobicity at Small and Large Length Scales
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The Mechanism of Hydrophobic Solvation Depends on Solute Radius
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Surface topography dependence of biomolecular hydrophobic hydration
inferredcites →https://doi.org/10.1038/35054591openalex-snapshot
Three key residues form a critical contact network in a protein folding transition state
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Interfaces and the driving force of hydrophobic assembly
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From Levinthal to pathways to funnels
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The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments
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The kinetics of folding of frataxin
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A general purpose model for the condensed phases of water: TIP4P/2005
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Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
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On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method
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Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle
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Relationship of Leffler (Brønsted) α values and protein folding Φ values to position of transition-state structures on reaction coordinates
inferredcites →https://doi.org/10.1073/pnas.0902778106openalex-snapshot
Characterizing hydrophobicity of interfaces by using cavity formation, solute binding, and water correlations
inferredcites →https://doi.org/10.1073/pnas.1108486108openalex-snapshot
Simplifying the representation of complex free-energy landscapes using sketch-map
inferredcites →https://doi.org/10.1073/pnas.111158498openalex-snapshot
Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water
inferredcites →https://doi.org/10.1073/pnas.1313006111openalex-snapshot
Temperature-dependent solvation modulates the dimensions of disordered proteins
inferredcites →https://doi.org/10.1073/pnas.92.24.10869openalex-snapshot
Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications.
inferredcites →https://doi.org/10.1073/pnas.92.8.3626openalex-snapshot
Toward an outline of the topography of a realistic protein-folding funnel.
inferredcites →https://doi.org/10.1080/07391102.2015.1032783openalex-snapshot
150 Water near proteins and interfaces: a new molecular perspective
inferredcites →https://doi.org/10.1103/physrevlett.100.020603openalex-snapshot
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
inferredcites →https://doi.org/10.1103/physrevlett.115.108101openalex-snapshot
Contribution of Water to Pressure and Cold Denaturation of Proteins
inferredcites →https://doi.org/10.1103/physrevlett.76.928openalex-snapshot
Effect of Environment on Hydrogen Bond Dynamics in Liquid Water
inferredcites →https://doi.org/10.1126/science.1096205openalex-snapshot
The Structure of the First Coordination Shell in Liquid Water
inferredcites →https://doi.org/10.1142/10574openalex-snapshot
Structure and Mechanism in Protein Science
inferredcites →https://doi.org/10.1146/annurev.biophys.34.040204.144517openalex-snapshot
MODELING WATER, THE HYDROPHOBIC EFFECT, AND ION SOLVATION
inferredcites →https://doi.org/10.1146/annurev.biophys.35.040405.102134openalex-snapshot
WATER MEDIATION IN PROTEIN FOLDING AND MOLECULAR RECOGNITION
inferredcites →https://doi.org/10.1146/annurev.physchem.58.032806.104445openalex-snapshot
Dewetting and Hydrophobic Interaction in Physical and Biological Systems
inferredcites →https://doi.org/10.1146/annurev.physchem.59.032607.093815openalex-snapshot
Water in Nonpolar Confinement: From Nanotubes to Proteins and Beyond
inferredcites →https://doi.org/10.1371/journal.pcbi.1003406openalex-snapshot
Combining Experiments and Simulations Using the Maximum Entropy Principle
inferredcites →https://doi.org/10.2174/1877946811202010079openalex-snapshot
Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations
inferredcites →https://doi.org/10.3109/10409239009090612openalex-snapshot
Cold Denaturation of Protein
inferredcites →https://doi.org/10.4236/abc.2013.31005openalex-snapshot
Theory of cold denaturation of proteins
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Accurate quantum-centric simulations of intermolecular interactions
inferred← citeshttps://doi.org/10.1039/c7cp08321aopenalex-snapshot
The fold preference and thermodynamic stability of α-synuclein fibrils is encoded in the non-amyloid-β component region
inferred← citeshttps://doi.org/10.1039/c8cp06513fopenalex-snapshot
Influence of glycerol on the cooling effect of pair hydrophobicity in water: relevance to proteins’ stabilization at low temperature
inferred← citeshttps://doi.org/10.1039/d0pp00145gopenalex-snapshot
In flow metal-enhanced fluorescence for biolabelling and biodetection
inferred← citeshttps://doi.org/10.1039/d0py00624fopenalex-snapshot
Nitroxide polymer gels for recyclable catalytic oxidation of primary alcohols to aldehydes
inferred← citeshttps://doi.org/10.1039/d1cc02786gopenalex-snapshot
Varying the hydrophobic spacer to influence multicomponent gelation
inferred← citeshttps://doi.org/10.1039/d2cp01650hopenalex-snapshot
Mechanistic insight into functionally different human islet polypeptide (hIAPP) amyloid: the intrinsic role of the C-terminal structural motifs
inferred← citeshttps://doi.org/10.1039/d3gc03680dopenalex-snapshot
Organic transformation of lignin into mussel-inspired glues: next-generation 2K adhesive for setting corals under saltwater
inferred← citeshttps://doi.org/10.1039/d3sc05828jopenalex-snapshot
Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder
inferred← citeshttps://doi.org/10.1039/d4fo05630bopenalex-snapshot
The effects of different thermal processing methods on the protein structure and digestibility of Procambarus clarkii
inferred← citeshttps://doi.org/10.1039/d5sm00207aopenalex-snapshot
Surfactant-driven modifications in protein structure
inferred← citeshttps://doi.org/10.1042/bcj20200462openalex-snapshot
Structure-based drug repurposing to inhibit the DNA gyrase of Mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1063/1.5019239openalex-snapshot
How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction
inferred← citeshttps://doi.org/10.1063/1.5031005openalex-snapshot
The spatial range of protein hydration
inferred← citeshttps://doi.org/10.1063/1.5037571openalex-snapshot
Solvent-mediated interactions between nanostructures: From water to Lennard-Jones liquid
inferred← citeshttps://doi.org/10.1063/5.0300133openalex-snapshot
Unveiling the entropic role of hydration water in SOD1 partitioning within FUS condensate
inferred← citeshttps://doi.org/10.1073/pnas.1703781114openalex-snapshot
Water is an active matrix of life for cell and molecular biology
inferred← citeshttps://doi.org/10.1074/jbc.ra120.015645openalex-snapshot
Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins
inferred← citeshttps://doi.org/10.1080/00914037.2018.1452222openalex-snapshot
Matricryptic peptide-inspired hydrogels for promoting osteogenic differentiation
inferred← citeshttps://doi.org/10.1080/07391102.2018.1454852openalex-snapshot
Drug targeted virtual screening and molecular dynamics of LipU protein of Mycobacterium tuberculosis and Mycobacterium leprae
inferred← citeshttps://doi.org/10.1080/07391102.2019.1621211openalex-snapshot
Unprecedented hydrophobic stabilizations from a reverse wobble T·T mispair in DNA minidumbbell
inferred← citeshttps://doi.org/10.1080/07391102.2020.1751295openalex-snapshot
Understanding the thermal response of rice eukaryotic transcription factor eIF4A1 towards dynamic temperature stress: insights from expression profiling and molecular dynamics simulation
inferred← citeshttps://doi.org/10.1080/07391102.2023.2227709openalex-snapshot
Understanding the structural basis of the binding specificity of c-di-AMP to M. smegmatis RecA using computational biology approach
inferred← citeshttps://doi.org/10.1080/19420862.2022.2080628openalex-snapshot
Separating clinical antibodies from repertoire antibodies, a path to in silico developability assessment
inferred← citeshttps://doi.org/10.1080/23746149.2018.1477531openalex-snapshot
Advanced simulation techniques for the thermodynamic and kinetic characterization of biological systems
inferred← citeshttps://doi.org/10.1088/1674-1056/ac1e21openalex-snapshot
Effect of an electric field on dewetting transition of nitrogen-water system
inferred← citeshttps://doi.org/10.1093/bib/bbad065openalex-snapshot
A review of enzyme design in catalytic stability by artificial intelligence
inferred← citeshttps://doi.org/10.1093/bib/bbae458openalex-snapshot
Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1
inferred← citeshttps://doi.org/10.1093/database/baag011openalex-snapshot
BEDB: a comprehensive binding energy database for molecular docking and dynamics: insights into Human Metapneumovirus (HMPV) Inhibitors
inferred← citeshttps://doi.org/10.1093/nar/gkad692openalex-snapshot
Strategies to identify and edit improvements in synthetic genome segments episomally
inferred← citeshttps://doi.org/10.1103/physrevx.7.021047openalex-snapshot
Role of Water in the Selection of Stable Proteins at Ambient and Extreme Thermodynamic Conditions
inferred← citeshttps://doi.org/10.1109/csitss64042.2024.10816928openalex-snapshot
Quantum Algorithmic Approaches to Protein Folding: A Comprehensive Study of Diverse Lattice Structures
inferred← citeshttps://doi.org/10.1126/sciadv.abb5924openalex-snapshot
Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease
inferred← citeshttps://doi.org/10.1134/s0006297918140043openalex-snapshot
The Molten Globule Concept: 45 Years Later
inferred← citeshttps://doi.org/10.11606/t.99.2019.tde-30092019-085345openalex-snapshot
Desenvolvimento do nanoimunossensor-AQP461-70 para o diagnóstico altamente específico e sensível de doenças do espectro da neuromielite óptica
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1013783openalex-snapshot
DDGWizard: Integration of feature calculation resources for analysis and prediction of changes in protein thermostability upon point mutations
inferred← citeshttps://doi.org/10.1371/journal.pone.0349143openalex-snapshot
Computational models for the classification of antibody specificity using heavy chain features
inferred← citeshttps://doi.org/10.1515/9783111122991-004openalex-snapshot
87Chapter 4 Medium Engineering
inferred← citeshttps://doi.org/10.17582/journal.pjz/20191216081232openalex-snapshot
Adaptive Mutations in Nuclear Export Protein and Non-Structural 1 Protein of Avian Influenza a H9N2 Virus Circulating in Punjab, Pakistan
inferred← citeshttps://doi.org/10.18297/etd/3787openalex-snapshot
Computational and biochemical characterizations of anhydrobiosis-related intrinsically disordered proteins.
inferred← citeshttps://doi.org/10.21203/rs.3.rs-7756125/v1openalex-snapshot
Discovery of Thermophilic Enzyme Properties Through Structural Modeling, Phylogenetic Analysis, and Machine Learning Prediction
inferred← citeshttps://doi.org/10.2210/pdb6a4o/pdbopenalex-snapshot
HEWL crystals soaked in 2.5M GuHCl for 20 minutes
inferred← citeshttps://doi.org/10.24275/uami.76537140zopenalex-snapshot
Evaluación de la estabilidad inducida a través de puentes salinos interdominio: un estudio de la enzima lacasa de Trametes versicolor
inferred← citeshttps://doi.org/10.33540/604openalex-snapshot
Programming supramolecular peptide materials for immunological applications
inferred← citeshttps://doi.org/10.3390/biomedicines10020425openalex-snapshot
Protein Mutations and Stability, a Link with Disease: The Case Study of Frataxin
inferred← citeshttps://doi.org/10.3390/foods14213662openalex-snapshot
Salting-Out Effect Behavior of Protein/λ-Carrageenan Composite Gels Enhanced by Enzymatic Pretreatment: Focusing on Microstructure, Interactions and the Potential for Dysphagia Food
inferred← citeshttps://doi.org/10.3390/ijms22179350openalex-snapshot
Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions
inferred← citeshttps://doi.org/10.3390/ijms22179653openalex-snapshot
Entropy-Enthalpy Compensations Fold Proteins in Precise Ways
inferred← citeshttps://doi.org/10.3390/ijms241713158openalex-snapshot
Glutaryl-CoA Dehydrogenase Misfolding in Glutaric Acidemia Type 1
inferred← citeshttps://doi.org/10.3390/ijms25179586openalex-snapshot
Dominant Chemical Interactions Governing the Folding Mechanism of Oligopeptides
inferred← citeshttps://doi.org/10.3390/ijms251810164openalex-snapshot
Mechanical Properties of a Solvated Biomolecule: RGD (1FUV) Peptide
inferred← citeshttps://doi.org/10.3390/ijms26157586openalex-snapshot
ZNF496 as Candidate Gene for Neurodevelopmental Disorders: Identification of a Pathogenic De Novo Frameshift Variant
inferred← citeshttps://doi.org/10.3390/microorganisms12020377openalex-snapshot
Improvement of Carotenoids’ Production by Increasing the Activity of Beta-Carotene Ketolase with Different Strategies
inferred← citeshttps://doi.org/10.3390/microorganisms13112455openalex-snapshot
Thermostable Proteases from Geobacillus: Production, Characterization, Structural Stability Mechanisms and Biotechnological Applications
inferred← citeshttps://doi.org/10.3390/molecules27144361openalex-snapshot
The Molten Globule State of a Globular Protein in a Cell Is More or Less Frequent Case Rather than an Exception
inferred← citeshttps://doi.org/10.3390/molecules27207009openalex-snapshot
The Hydrophobic Effects: Our Current Understanding
inferred← citeshttps://doi.org/10.3390/ph18111711openalex-snapshot
Protein Representation in Metric Spaces for Protein Druggability Prediction: A Case Study on Aspirin
inferred← citeshttps://doi.org/10.3390/polym16233273openalex-snapshot
Preliminary In Vitro Assessment of Whey Protein Isolate Hydrogel with Cannabidiol as a Potential Hydrophobic Oral Drug Delivery System for Colorectal Cancer Therapy
inferred← citeshttps://doi.org/10.36062/ijah.2021.08321openalex-snapshot
In silico analysis of bovine Glutathione-S-transferase M1 (GSTM1), an essential gene governing bull semen quality
inferred← citeshttps://doi.org/10.36062/ijah.2022.14022openalex-snapshot
In-silico ab initio 3D structure prediction of goat kisspeptin precursor protein (135 amino acid residues)
inferred← citeshttps://doi.org/10.4236/aer.2019.71001openalex-snapshot
Enzymatic Hydrolysis of an Organic Sulfur Compound
inferred← citeshttps://doi.org/10.5059/yukigoseikyokaishi.81.1103openalex-snapshot
Novel Estrogen Receptor Inhibitory Mechanism for Halogen-containing Endocrine-disrupting Chemicals Discovered by Computer Simulation
inferred← citeshttps://doi.org/10.56499/jppres23.1891_12.4.735openalex-snapshot
In silico studies of Ruellia tuberosa L. compounds as aldose reductase, dipeptidyl peptidase 4, and α-glucosidase inhibitors against type 2 diabetes mellitus
inferred← citeshttps://doi.org/10.5772/intechopen.97603openalex-snapshot
Probing Biological Water Using Terahertz Absorption Spectroscopy
inferred← citeshttps://doi.org/10.64898/2026.05.18.725793openalex-snapshot
CharacTERT: A Machine Learning Tool for Classifying hTERT Missense Variants
inferred← citeshttps://doi.org/10.70322/sbe.2025.10001openalex-snapshot
High-Temperature Catalytic Platform Powered by Thermophilic Microorganisms and Thermozymes
inferred← citeshttps://doi.org/10.70675/8d030170zb542z43f3z8ecfz023b75634f87openalex-snapshot
Adaptive biasing algorithms : mathematical analysis and applications in molecular dynamics
inferred← citeshttps://doi.org/10.70675/fd141c5fz0b58z443ez9904zfe9e99196053openalex-snapshot
Characterization of Arenaviridae nucleases and design of inhibitors
inferred← citeshttps://doi.org/10.7554/elife.111124openalex-snapshot
Role of desolvation on biomolecular liquid–liquid phase separation
inferred← citeshttps://doi.org/10.7554/elife.111124.1openalex-snapshot
Role of desolvation on biomolecular liquid-liquid phase separation
inferred← citeshttps://doi.org/10.7554/elife.111124.2openalex-snapshot
Role of desolvation on biomolecular liquid-liquid phase separation
inferred← citeshttps://doi.org/10.7554/elife.111124.3openalex-snapshot
Role of desolvation on biomolecular liquid–liquid phase separation
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