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Conformational dynamics and molecular interactions of natural products: unveiling functional structures in biological membranes

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Copper pincer targets SARS-CoV-2 Omicron, Delta, and Wild-Type receptor binding domains

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Compensation relationship in thermodynamics of gas-phase molecular complexation

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Configurational space discretization and free energy calculation in complex molecular systems

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Moderate point: Balanced entropy and enthalpy contributions in soft matter

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Can Simple Interaction Models Explain Sequence-Dependent Effects in Peptide Homodimerization?

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Identification of Aspergillus fumigatus UDP-Galactopyranose Mutase Inhibitors

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Cross effects of structure and temperature in the reactions of trans-2,3-diaryloxiranes with arenesulfonic acids

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Bacterial Porins

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Non-electrostatic interactions associated with aggregate formation between polyallylamine and Escherichia coli

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Albumin Promotes the Absorption of Pb in the Intestine: A Possible Pathway Linking to the High Absorption of Pb in Adolescence

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Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease

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Structural plasticity of omicron BA.5 and BA.2.75 for enhanced ACE-dependent entry into cells

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Identification of Hydrophobic Interfaces in Protein-Ligand Complexes by Selective Saturation Transfer NMR Spectroscopy

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Inhibition of cMYC-MAX transcription factors hetero-dimerization with structurally engineered omoMYC to downregulate oncogenic pathways in renal carcinoma

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Identification and Analysis of Ardisia humilis as Potential Antihyperlipidemic by Network Pharmacology Followed by Molecular Docking

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Screening of medicinal phytocompounds with structure-based approaches to target key hotspot residues in tyrosyl-DNA phosphodiesterase 1: augmenting sensitivity of cancer cells to topoisomerase I inhibitors

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Thermodynamics of Molecular Transport Through a Nanochannel: Evidence of Energy–Entropy Compensation

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Thermodynamic signatures in macromolecular interactions involving conformational flexibility

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Exploring the impact of the side-chain length on peptide/RNA binding events

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Noncovalent Interactions in Biocatalysis – A Theoretical Perspective

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Structural and dynamic investigation of non‐synonymous variations in Renin–AGT complex revealed altered binding via hydrogen‐bonding network reprogramming to accelerate the hypertension pathway

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Analysis of E2F1 single-nucleotide polymorphisms reveals deleterious non-synonymous substitutions that disrupt E2F1-RB protein interaction in cancer

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Enhancing carbohydrate binding module family 40 (CBM40) via in silico sequential mutagenesis approach

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Stabilization of a protein by a single halogen‐based aromatic amplifier

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Exploring MERTK inhibitor binding mechanisms: insights from adaptive steered molecular dynamics and free energy calculation

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Probabilistic model to treat flexibility in molecular contacts

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The origin of extrathermodynamic compensations

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Time-dependent conformational analysis of ALK5-lumican complex in presence of graphene and graphene oxide employing molecular dynamics and MMPBSA calculation

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Evaluation of Binding Kinetics and Thermodynamics of Antibody–Antigen Interactions and Interactions Involving Complement Proteins

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Revealing the dynamics and energetics of interaction of a cationic biological photosensitizer within a bile salt aggregate

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Thermodynamic profiles of the interactions of suramin, chondroitin sulfate, and pentosan polysulfate with the inhibitory domain of TIMP ‐3

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Assessing the Recyclability of Supramolecularly Assembled Organocatalytic Species: A Theoretical Insight

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Developing Small Molecule Inhibitors of ALK2: A Serine/Threonine Kinase Implicated in Diffuse Intrinsic Pontine Glioma

Ensan, D. (2020) · TSpace (University of Toronto) · Cited by 2

Making sense of chaos: uncovering the mechanisms of conformational entropyPreprint

Wankowicz, S. A. M., & Fraser, J. S. (2024) · ChemRxiv · doi:10.26434/chemrxiv-2023-9b5k7-v2 · Cited by 1

The functional role of the hemoglobin-water interface

Meuwly, M., & Karplus, M. (2021) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2021.101042 · Cited by 1

Structural Biology for Target Identification and Validation

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ML-Driven Approach to Discovery of Peptide-Based BACE1 Inhibitors

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Computational Tools for Solubility Prediction

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Calculations of the Absolute Free Energy, Enthalpy, and Entropy of Drug Binding Using Different Potential Models.

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Digital design and discovery of biological metal–organic frameworks for gas signaling

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Revealing and Distinguishing the Binding Sites of Agonists/Antagonists on the MrgprX2 by CMC-MD Strategy

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Non-covalent Interactions at the QM–MM Interface in the Semiempirical and Density Functional Limit

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Consequences of Peptide Macrocyclization Revealed by Virus-Inspired β-Hairpin Mimetics

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Unveiling the role of ZIKV NS4A mutants F4L and E8D through molecular docking and dynamics simulation: implications for MAVS-mediated immune evasion

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Three-Dimensional Case in Solvation Thermodynamics: Variation of Temperature, Transfer Route, and Thermodynamic Function

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Computational hybrid framework integrating clinical-mutation profiling and physics-based simulations to predict structural tolerance of Bruton tyrosine kinase (BTK) and sustained ARQ 531 binding

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An explainable machine learning-based scoring function using interpretable features and model explanation approaches for binding affinity prediction

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Molecular dynamics simulations of temperature-dependent PET binding in PETase, ThermoPETase, and FAST-PETase

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Frontiers and challenges in the design of binders for intrinsically disordered proteins

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Intramolecular bonding as a design strategy for robust intermolecular binding of oligomers

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Integrated in silico and in vivo larvicidal evaluation of compounds targeting juvenile hormone for malaria vector control

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Non-Monotonic Interfacial Layering at Water/[C n mim][TFSA] Interfaces Associated with Entropy–Enthalpy Compensation

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Synthesis and Kinetic Analysis of Two Conformationally Restricted Peptide Substrates of Escherichia coli Penicillin-Binding Protein 5

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A combined variable temperature 600 MHz NMR/MD study of the calcium release agent cyclic adenosine diphosphate ribose (cADPR): Structure, conformational analysis, and thermodynamics of the conformational equilibria

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Effects of hydrocortisone-presensitized sugammadex on recovery from neuromuscular blockade induced by rocuronium: a rodent in vivo study

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Analysis of the bonding affinities between human PSGL-1 and Vpu derived from the different HIV-1 groups – in silico insights

Zaongo, S. D., Rashid, F., Suleman, M., Harypursat, V., Song, F., & Chen, Y.-K. (2025) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2025.2500682 · Cited by 1

Functionalized Polymeric Nanoparticles for Yttrium Recovery by Chelating Effect

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Profiling Drug Binding by Thermodynamics

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Accurate Estimation of Protein-ligand Binding Free Energies Based on Geometric Restraints

Fu, H., Chen, H., Zhang, H., Shao, X., & Cai, W. (2021) · 化学学报 · doi:10.6023/a20100489 · Cited by 1

Water in Enzyme Catalysis as a Promoter and Chemical Reagent

Likhtenshtein, G. I. (2021) · Soft and biological matter · doi:10.1007/978-3-030-82503-4_8 · Cited by 1

Probing the ligand-binding pocket of recombinant β-lactoglobulin: Calorimetric and spectroscopic studies

Bonarek, P., Mularczyk, D., Loch, J. I., & Dziedzicka‐Wasylewska, M. (2022) · Biophysical Chemistry · doi:10.1016/j.bpc.2022.106770 · Cited by 1

Theoretical Insights into the Reduction of Azurin Metal Site with Unnatural Amino Acid Substitutions

Yang, W., & Li, P. (2023) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2024.112651 · Cited by 1

Conformational Dynamics Associated with Ligand Binding to Vertebrate Hexa-coordinate Hemoglobins

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Additivity of Energy Contributions in Multivalent Complexes

Schneider, H. (2017) · doi:10.1002/9781119143505.ch1 · Cited by 1

Predictive Modelling of the Primary and Secondary Pharmacology of Compounds in Drug Discovery

Giblin, K. A. (2019) · Apollo (University of Cambridge) · doi:10.17863/cam.50088 · Cited by 1

Binding of Phenothiazine Drugs to Heptakis-Methylated β-Cyclodextrin Derivatives: Thermodynamics and StructurePreprint

Andrade, B., Chen, A., & Gilson, M. K. (2023) · ChemRxiv · doi:10.26434/chemrxiv-2023-z5tcm-v2 · Cited by 1

Thermodynamic Profiling of Carbonic Anhydrase Inhibitors

Jones, L. H. (2015) · Methods and principles in medicinal chemistry · doi:10.1002/9783527673025.ch7

Conformational Dynamics of Cytochrome P450cam Upon Ligand Binding

Gomez, B., & Virgínia, A. (2015)

Thermodynamics‐Guided Optimizations in Medicinal Chemistry

Keserű, G. M. (2015) · Methods and principles in medicinal chemistry · doi:10.1002/9783527673025.ch4

Thermodynamics in Lead Optimization

Holdgate, G. A., Scott, A., & Davies, G. M. (2015) · Methods and principles in medicinal chemistry · doi:10.1002/9783527673025.ch6

Conformational Dynamics and Stability Associated with Magnesium or Calcium Binding to DREAM in the Regulation of Interactions between DREAM and DNA or Presenilins

Pham, K. (2016) · doi:10.25148/etd.fidc000735

Surface Plasmon Resonance for Identifying and Characterising Small Molecule Ligands

Pollack, S. J. (2017) · Royal Society of Chemistry eBooks · doi:10.1039/9781788010016-00170

Determinação da afinidade e assinatura termodinâmica de inibidores da cruzaína por calorimetria de titulação isotérmica

Prokopczyk, I. M. (2016) · doi:10.11606/t.75.2016.tde-09112016-153328

Effect of ultraviolet/visible radiation processing on the quality of fruit juices

Aguilar, K. (2017) · Repositori ObertUDL (University of Lleida)

A hydrophobic-interaction-based mechanism trigger docking between the SARS CoV 2 spike and angiotensin-converting enzyme 2Preprint

Li, J., Ma, X., Guo, S., Hou, C., Shi, L., Zhang, H., Zheng, B., Liao, C., Yang, L., Ye, L., et al. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2008.11883

Entropy deepens loading chemical potentials of small alcohols by narrow carbon nanotubes

Barria‐Urenda, M., & Gárate, J. A. (2020) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp03426f

Síntese de inibidores da cisteíno protease cruzaína e estudo de relação estrutura-atividade

da Silva, M. A. G. (2021) · doi:10.11606/d.75.2021.tde-04052021-112441

Faculty Opinions recommendation of Crystal structure of a photosynthetic LH1-RC in complex with its electron donor HiPIP.

Allen, J. P. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.739584742.793585631

Fluorogenesis: Inducing Fluorescence in a Non-Fluorescent Protein Through Photoinduced Chromophore Transfer of a Genetically Encoded ChromophorePreprint

Kumar, Y., Singh, R. K., Ojha, M., & Pushpavanam, K. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.24.546416

Comprehensive analysis unveils altered binding kinetics of 5-/6-methylCytosine/adenine modifications in R2R3-DNA system

Wang, Q., Luo, S., Xiong, D., Xu, X., Wang, L., & Duan, L. (2023) · Physical Chemistry Chemical Physics · doi:10.1039/d3cp02544f

Tetra‐ and Hexavalent Siglec‐8 Ligands Modulate Immune Cell Activation

Conti, G., Bärenwaldt, A., Rabbani, S., Mühlethaler, T., Sarcevic, M., Jiang, X., Schwardt, O., Ricklin, D., Pieters, R. J., Laubli, H. P., et al. (2023) · Angewandte Chemie · doi:10.1002/ange.202314280

Design and Thermodynamics Principles to Program the Cooperativity of Molecular Assemblies

Lauzon, D., & Vallée‐Bélisle, A. (2023) · Angewandte Chemie International Edition · doi:10.1002/anie.202313944

Identification of potential 3CLpro inhibitors-modulators for human norovirus infections: An advanced virtual screening approachPreprint

Bhowmick, S., Mistri, T. K., Okla, M. K., Saleh, I. A. S., AbdElgawad, H., Saha, A., & Patil, P. C. (2023) · Research Square · doi:10.21203/rs.3.rs-3614758/v1

Design and Thermodynamics Principles to Program the Cooperativity of Molecular Assemblies

Lauzon, D., & Vallée‐Bélisle, A. (2023) · Angewandte Chemie · doi:10.1002/ange.202313944

Investigando a especificidade e inibição da principal protease do SARS-CoV-2 e suas variantes

Rocho, F. D. R. (2023) · doi:10.11606/t.75.2023.tde-29012024-111014

Effect of computationally designed fragment-based analogs on the RBD–ACE2 complex of the SARS-CoV-2 P.1 variant

Lata, S., & Akif, M. (2024) · Molecular Systems Design & Engineering · doi:10.1039/d3me00193h

New computational methods to study the relationship between protein structure and function

Kumar, A. (2022) · doi:10.31274/td-20240329-537

Interation between Polycyclic Aromatic Hydrocarbons and Thymine (T)-Base Induces Double-Stranded DNA Distortion in Different SpeciesPreprint

Liu, X., Wu, J., He, S., Ge, F., & Liu, N. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4789630

Complexity associated with caprylate binding to bovine serum albumin: Dimerization, allostery, and variance between the change in free energy and enthalpy of binding

Capili, M. J. A., Oerlemans, S. K., Wright, L., & Falconer, R. J. (2024) · Protein Science · doi:10.1002/pro.5224

Assessment of the Topology and OligomerisationStates of Coiled Coils Using Metadynamics withConformational RestraintsPreprint

Notari, E., Wood, C. W., & Michel, J. (2024) · ChemRxiv · doi:10.26434/chemrxiv-2024-t02df

Progress in the understanding of traditional and nontraditional molecular interactions

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