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Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf

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Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization

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Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations

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Integrative approaches in HIV ‐1 non‐nucleoside reverse transcriptase inhibitor design

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Ultrahigh binding affinity of a hydrocarbon guest inside cucurbit[7]uril enhanced by strong host–guest charge matching

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Thermodynamic Analysis of the Uptake of a Protein in a Spherical Polyelectrolyte Brush

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Absolute Binding Free Energy Calculations for Highly Flexible Protein MDM2 and Its Inhibitors

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Effect of Stapling on the Thermodynamics of mdm2–p53 Binding

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A rational search for discovering potential neutraligands of human complement fragment 5a (hC5a)

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Avoiding accuracy-limiting pitfalls in the study of protein-ligand interactions with isothermal titration calorimetryPreprint

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Structural and molecular insights into the mechanism of resistance to enzalutamide by the clinical mutants in androgen receptor (AR) in castration-resistant prostate cancer (CRPC) patients

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Salvianolic acid B inhibits thrombosis and directly blocks the thrombin catalytic site

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Measuring the bioactivity and molecular conformation of typically globular proteins with phenothiazine-derived methylene blue in solid and in solution: A comparative study using photochemistry and computational chemistry

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Understanding PIM-1 kinase inhibitor interactions with free energy simulation

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Identification of a new series of potent diphenol HSP90 inhibitors by fragment merging and structure-based optimization

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Structural and ITC Characterization of Peptide‐Protein Binding: Thermodynamic Consequences of Cyclization Constraints, a Case Study on Vascular Endothelial Growth Factor Ligands

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On Enthalpy–Entropy Compensation Characterizing Processes in Aqueous Solution

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Polyvalent Glycan Quantum Dots as a Multifunctional Tool for Revealing Thermodynamic, Kinetic, and Structural Details of Multivalent Lectin–Glycan Interactions

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Vascular Endothelial Growth Factor Peptide Ligands Explored by Competition Assay and Isothermal Titration Calorimetry

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Thermodynamic Proxies to Compensate for Biases in Drug Discovery Methods

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Entropic control of the free-energy landscape of an archetypal biomolecular machine

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Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method

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Solvation Thermodynamics in Different Solvents: Water–Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory

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The effect of protein mutations on drug binding suggests ensuing personalised drug selection

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Entropy-enthalpy compensation in conjugated proteins

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Intrinsically disordered protein NUPR1 binds to the armadillo-repeat domain of Plakophilin 1

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Ligand Binding Introduces Significant Allosteric Shifts in the Locations of Protein Fluctuations

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Pillar[n]arenes and Other Cavitands: Aspects of Complex Thermodynamics

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Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies

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Thermodynamic profiling for fragment-based lead discovery and optimization

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Sequence-structure functional implications and molecular simulation of high deleterious nonsynonymous substitutions in IDH1 revealed the mechanism of drug resistance in glioma

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Concentration‐, Temperature‐ and Solvent‐Dependent Self‐Assembly: Merocyanine Dimerization as a Showcase Example for Obtaining Reliable Thermodynamic Data

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Febrile temperatures increase in vitro antibody affinity for malarial and dengue antigens

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Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure

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A thermodynamic study of reactions of amino acids with crown ethers in nonaqueous media as examples of guest—host molecular complex formation

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Near-exact enthalpy–entropy compensation governs the thermal unfolding of protonation states of oxidized cytochrome c

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The importance of ionic hydration in the transport of monovalent anions through nanofiltration membranes

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Thermodynamics of Binding of Structurally Similar Ligands to Histone Deacetylase 8 Sheds Light on Challenges in the Rational Design of Potent and Isozyme-Selective Inhibitors of the Enzyme

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The role of NMR in leveraging dynamics and entropy in drug design

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Rate-acidity hysteresis and enthalpy-entropy compensation upon metalloporphyrin formation: Implication for the metal ion coordination mechanism

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Investigating the Impact of Hydrophobic Polymer Segments on the Self-Assembly Behavior of Supramolecular Cyclic Peptide Systems via Asymmetric-Flow Field Flow Fractionation

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V Region of IgG Controls the Molecular Properties of the Binding Site for Neonatal Fc Receptor

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A protein coupling and molecular simulation analysis of the clinical mutants of androgen receptor revealed a higher binding for Leupaxin, to increase the prostate cancer invasion and motility

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Cucurbit[n]urils (n = 7, 8) can strongly bind neutral hydrophilic molecules in water

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Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites

Marsh, L. (2015) · BioMed Research International · doi:10.1155/2015/746980 · Cited by 14

Kinetics, Thermodynamics, and Ligand Efficiency Metrics in Drug Discovery

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Are We There Yet? Applying Thermodynamic and Kinetic Profiling on Embryonic Ectoderm Development (EED) Hit-to-Lead Program

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Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site

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Thermodynamic analysis of the solubility of progesterone in 1-octanol + ethanol cosolvent mixtures at different temperatures

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Contemporary biophysical approaches for studying 14-3-3 protein-protein interactions

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The role of loop dynamics in the prediction of ligand–protein binding enthalpy

Çınaroğlu, S. S., & Biggin, P. C. (2023) · Chemical Science · doi:10.1039/d2sc06471e · Cited by 14

A role for conformational changes in enzyme catalysis

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Understanding Aldose Reductase-Inhibitors interactions with free energy simulation

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“Register-shift” insulin analogs uncover constraints of proteotoxicity in protein evolution

Rege, N. K., Liu, M. R., Dhayalan, B., Chen, Y., Smith, N. A., Rahimi, L., Sun, J., Guo, H., Yang, Y., Haataja, L., et al. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.011389 · Cited by 12

Compensation relationship in thermodynamics of solvation and vaporization: Features and applications. I. Non-hydrogen-bonded systems

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Numerical Analysis of Sulfamerazine Solubility in Acetonitrile + 1-Propanol Cosolvent Mixtures at Different Temperatures

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Entropic and Enthalpic Contributions to Stereospecific Ligand Binding from Enhanced Sampling Methods

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Chiral macrocycles forming high-affinity host-guest homoternary complexes for chiral discrimination and amplified circularly polarized luminescence

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Insights into Modeling Approaches in Chemistry: Assessing Ligand‐Protein Binding Thermodynamics Based on Rigid‐Flexible Model Molecules

Komarov, I. V., Bugrov, V., Cherednychenko, A., & Grygorenko, O. O. (2023) · The Chemical Record · doi:10.1002/tcr.202300276 · Cited by 12

In vitro and in silico Anti-diabetes mechanism of phytochemicals from Curculigo pilosa and its pharmacokinetic profiling via α-amylase inhibition

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Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation

Sun, Z., Wang, X., & Zhang, J. Z. H. (2019) · Chemical Physics Letters · doi:10.1016/j.cplett.2019.03.020 · Cited by 12

Quantum Chemical Calculations on Two Compounds of Proquazone and Proquazone Type Calcites as a Calcium Sensing Receptor (CaSR) Inhibitory Profiles

Shntaif, A. H., Rashid, Z. M., Al-Sawaff, Z. H., & Kandemi̇rlı, F. (2021) · Russian Journal of Bioorganic Chemistry · doi:10.1134/s106816202103016x · Cited by 12

DHFR Mutants Modulate Their Synchronized Dynamics with the Substrate by Shifting Hydrogen Bond Occupancies

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Toward Reliable and Insightful Entropy Calculations on Flexible Molecules

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Thermodynamic Assessment of Triclocarban Dissolution Process in N-Methyl-2-pyrrolidone + Water Cosolvent Mixtures

Rubio, D. I. C., Ortíz, C. P., R., F. M., & Delgado, D. R. (2023) · Molecules · doi:10.3390/molecules28207216 · Cited by 12

Thermodynamic investigation of the interaction between cyclodextrins and preservatives — Application and verification in a mathematical model to determine the needed preservative surplus in aqueous cyclodextrin formulations

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Entropy–enthalpy compensation at the single protein level: pH sensing in the bacterial channel OmpF

Alcaraz, A., Queralt-Martín, M., Verdiá-Báguena, C., Aguilella, V. M., & Mafé, S. (2014) · Nanoscale · doi:10.1039/c4nr03811h · Cited by 11

Some Thermodynamic Effects of Varying Nonpolar Surfaces in Protein-Ligand Interactions.

Cramer, D. L., Cheng, B., Tian, J.-H., Clements, J. H., Wypych, R. M., & Martin, S. (2020) · European journal of medicinal chemistry · doi:10.1016/j.ejmech.2020.112771 · Cited by 9

Differential interactions of two local anesthetics with phospholipid membrane and nonerythroid spectrin: Localization in presence of cholesterol and ganglioside, GM1

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Manipulating Excited-State Dynamics of Individual Light-Harvesting Chromophores through Restricted Motions in a Hydrated Nanoscale Protein Cavity

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Investigating Substitutions in Antibody–Antigen Complexes Using Molecular Dynamics: A Case Study with Broad-spectrum, Influenza A Antibodies

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Computational Peptide Design Cotargeting Glucagon and Glucagon-like Peptide-1 Receptors

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Interfacial water confers transcription factors with dinucleotide specificity

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Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations

Niazi, S. K. (2025) · Pharmaceuticals · doi:10.3390/ph18070951 · Cited by 11

Entropic Contributions to Protein Stability

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