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Free Energy, Entropy, and Induced Fit in Host−Guest Recognition: Calculations with the Second-Generation Mining Minima Algorithm
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Outgoing claims: the papers this work cites, builds on, or argues with.
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On the Theory of Noncovalent Binding
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Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration
inferred← citeshttps://doi.org/10.1021/ct401058wopenalex-snapshot
Variational Implicit Solvation with Poisson–Boltzmann Theory
inferred← citeshttps://doi.org/10.1021/ct500189sopenalex-snapshot
Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods
inferred← citeshttps://doi.org/10.1021/ct900668kopenalex-snapshot
Stress Analysis at the Molecular Level: A Forced Cucurbituril-Guest Dissociation Pathway
inferred← citeshttps://doi.org/10.1021/ja109904uopenalex-snapshot
New Ultrahigh Affinity Host−Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations
inferred← citeshttps://doi.org/10.1021/ja808175mopenalex-snapshot
Host−Guest Complexes with Protein−Ligand-like Affinities: Computational Analysis and Design
inferred← citeshttps://doi.org/10.1021/jacs.8b02993openalex-snapshot
Programmed Negative Allostery with Guest-Selected Rotamers Control Anion–Anion Complexes of Stackable Macrocycles
inferred← citeshttps://doi.org/10.1021/jacs.9b06926openalex-snapshot
Switching of Recognition First and Reaction First Mechanisms in Host–Guest Binding Associated with Chemical Reactions
inferred← citeshttps://doi.org/10.1021/jm049461bopenalex-snapshot
Rapid Computational Identification of the Targets of Protein Kinase Inhibitors
inferred← citeshttps://doi.org/10.1021/jm201371yopenalex-snapshot
Cellular Quantitative Structure–Activity Relationship (Cell-QSAR): Conceptual Dissection of Receptor Binding and Intracellular Disposition in Antifilarial Activities of Selwood Antimycins
inferred← citeshttps://doi.org/10.1021/jm800562dopenalex-snapshot
Target Flexibility: An Emerging Consideration in Drug Discovery and Design
inferred← citeshttps://doi.org/10.1021/jp110434sopenalex-snapshot
Symmetry Numbers for Rigid, Flexible, and Fluxional Molecules: Theory and Applications
inferred← citeshttps://doi.org/10.1021/jp204047bopenalex-snapshot
Elucidating the Energetics of Entropically Driven Protein–Ligand Association: Calculations of Absolute Binding Free Energy and Entropy
inferred← citeshttps://doi.org/10.1021/jp2068123openalex-snapshot
Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation
inferred← citeshttps://doi.org/10.1021/jp503319sopenalex-snapshot
Facet Selectivity of Ligands on Silver Nanoplates: Molecular Mechanics Study
inferred← citeshttps://doi.org/10.1021/jp506376zopenalex-snapshot
Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease
inferred← citeshttps://doi.org/10.1021/jp802460popenalex-snapshot
Calculation of Absolute Ligand Binding Free Energy to a Ribosome-Targeting Protein as a Function of Solvent Model
inferred← citeshttps://doi.org/10.1021/ol8018067openalex-snapshot
One-Pot Reaction as an Efficient Method for Rigid Molecular Tweezers
inferred← citeshttps://doi.org/10.1021/ol802199topenalex-snapshot
Encapsulation of Guests within a Gated Molecular Basket: Thermodynamics and Selectivity
inferred← citeshttps://doi.org/10.1038/s42004-024-01328-7openalex-snapshot
Accurate protein-ligand binding free energy estimation using QM/MM on multi-conformers predicted from classical mining minima
inferred← citeshttps://doi.org/10.1039/9781849735056-00281openalex-snapshot
Molecular Simulation in Computer-aided Drug Design: Algorithms and Applications
inferred← citeshttps://doi.org/10.1039/9781849735377-00023openalex-snapshot
Thermodynamics of Ligand Binding
inferred← citeshttps://doi.org/10.1039/b707955aopenalex-snapshot
Host-rotaxanes model proteins that promote ligand association through a favorable change in configurational entropy
inferred← citeshttps://doi.org/10.1039/b820487jopenalex-snapshot
Thermodynamics and structure of inclusion compounds of tauro- and glyco-conjugated bile salts and β-cyclodextrin
inferred← citeshttps://doi.org/10.1039/c1cp21779hopenalex-snapshot
Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature
inferred← citeshttps://doi.org/10.1039/c1ra00768hopenalex-snapshot
Cucurbituril chemistry: a tale of supramolecular success
inferred← citeshttps://doi.org/10.1039/c2ob26834eopenalex-snapshot
Probing the tolerance of cucurbit[7]uril inclusion complexes to small structural changes in the guest
inferred← citeshttps://doi.org/10.1039/c3md00038aopenalex-snapshot
A quantum chemical view of enthalpy–entropy compensation
inferred← citeshttps://doi.org/10.1039/c4cs00273copenalex-snapshot
Cucurbiturils: from synthesis to high-affinity binding and catalysis
inferred← citeshttps://doi.org/10.1039/c5cs00631gopenalex-snapshot
Can we beat the biotin–avidin pair?: cucurbit[7]uril-based ultrahigh affinity host–guest complexes and their applications
inferred← citeshttps://doi.org/10.1039/c5ob02641eopenalex-snapshot
Polar solvent effects on tartaric acid binding by aromatic oligoamide foldamer capsules
inferred← citeshttps://doi.org/10.1039/c6md00581kopenalex-snapshot
Protein–ligand (un)binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling
inferred← citeshttps://doi.org/10.1039/c9ce01190kopenalex-snapshot
The interplay among molecular structures, crystal symmetries and lattice energy landscapes revealed using unsupervised machine learning: a closer look at pyrrole azaphenacenes
inferred← citeshttps://doi.org/10.1039/c9cp00070dopenalex-snapshot
Understanding PIM-1 kinase inhibitor interactions with free energy simulation
inferred← citeshttps://doi.org/10.1039/c9sc04860jopenalex-snapshot
Tuning radical interactions in trisradical tricationic complexes by varying host-cavity sizes
inferred← citeshttps://doi.org/10.1039/d1cc03395fopenalex-snapshot
Solvation energetics of proteins and their aggregates analyzed by all-atom molecular dynamics simulations and the energy-representation theory of solvation
inferred← citeshttps://doi.org/10.1039/d1cp05075copenalex-snapshot
Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model
inferred← citeshttps://doi.org/10.1039/d2cp05839aopenalex-snapshot
An energy minimization strategy based on an improved nonlinear conjugate gradient method for accelerating the charged polymer dynamics simulation
inferred← citeshttps://doi.org/10.1039/d2sc05031eopenalex-snapshot
Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase
inferred← citeshttps://doi.org/10.1063/1.2174008openalex-snapshot
Simple estimation of absolute free energies for biomolecules
inferred← citeshttps://doi.org/10.1063/1.2746329openalex-snapshot
Extraction of configurational entropy from molecular simulations via an expansion approximation
inferred← citeshttps://doi.org/10.1063/1.3088434openalex-snapshot
Sampling conformations in high dimensions using low-dimensional distribution functions
inferred← citeshttps://doi.org/10.1063/1.3571441openalex-snapshot
Accelerated convergence of molecular free energy via superposition approximation-based reference states
inferred← citeshttps://doi.org/10.1063/1.4813627openalex-snapshot
Energy landscapes and global thermodynamics for alanine peptides
inferred← citeshttps://doi.org/10.1063/1.5019410openalex-snapshot
Probabilistic analysis for identifying the driving force of protein folding
inferred← citeshttps://doi.org/10.1063/1.5088395openalex-snapshot
Free-energy analysis of the hydration and cosolvent effects on the β-sheet aggregation through all-atom molecular dynamics simulation
inferred← citeshttps://doi.org/10.1063/5.0040759openalex-snapshot
Computation of host–guest binding free energies with a new quantum mechanics based mining minima algorithm
inferred← citeshttps://doi.org/10.1073/pnas.0610064104openalex-snapshot
Molecular evolution of affinity and flexibility in the immune system
inferred← citeshttps://doi.org/10.1073/pnas.0610494104openalex-snapshot
Ligand configurational entropy and protein binding
inferred← citeshttps://doi.org/10.1073/pnas.0706063105openalex-snapshot
A black-box re-weighting analysis can correct flawed simulation data
inferred← citeshttps://doi.org/10.1073/pnas.0706407105openalex-snapshot
A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy–entropy compensation
inferred← citeshttps://doi.org/10.1073/pnas.1208076109openalex-snapshot
Engineering a model protein cavity to catalyze the Kemp elimination
inferred← citeshttps://doi.org/10.1080/00268976.2018.1459002openalex-snapshot
Entropy of flexible liquids from hierarchical force–torque covariance and coordination
inferred← citeshttps://doi.org/10.1080/07391102.2016.1251851openalex-snapshot
Evaluation of protein–ligand affinity prediction using steered molecular dynamics simulations
inferred← citeshttps://doi.org/10.1080/08927022.2012.740636openalex-snapshot
Inclusion complexes of β-cyclodextrine with organic ligands: molecular dynamics simulation of the thermodynamic stability in gas phase and in water solution
inferred← citeshttps://doi.org/10.1080/10610278.2017.1415434openalex-snapshot
Chemodosimeters and chemoreactands for sensing ferric ions
inferred← citeshttps://doi.org/10.1146/annurev-biophys-083012-130318openalex-snapshot
Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design
inferred← citeshttps://doi.org/10.1146/annurev-physchem-052516-050843openalex-snapshot
Computer Simulations of Intrinsically Disordered Proteins
inferred← citeshttps://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
Calculation of Protein-Ligand Binding Affinities
inferred← citeshttps://doi.org/10.1177/1087057105281220openalex-snapshot
Virtual Ligand Screening against Escherichia coli Dihydrofolate Reductase: Improving Docking Enrichment Using Physics-Based Methods
inferred← citeshttps://doi.org/10.12691/ajmo-4-3-2openalex-snapshot
Docking and Ligand Binding Affinity: Uses and Pitfalls
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005057openalex-snapshot
Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design
inferred← citeshttps://doi.org/10.1517/17425255.2010.486399openalex-snapshot
Structural ensemble in computational drug screening
inferred← citeshttps://doi.org/10.1517/17460441.2010.523697openalex-snapshot
In silico fragment-based drug design
inferred← citeshttps://doi.org/10.1529/biophysj.104.049494openalex-snapshot
Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design
inferred← citeshttps://doi.org/10.1529/biophysj.105.071589openalex-snapshot
Calculation of Absolute Protein-Ligand Binding Affinity Using Path and Endpoint Approaches
inferred← citeshttps://doi.org/10.2142/biophysico.16.0_185openalex-snapshot
Energetics of cosolvent effect on peptide aggregation
inferred← citeshttps://doi.org/10.21608/bfsa.2022.239441openalex-snapshot
SYNTHESIS, MOLECULAR MODELING STUDY, AND BIOLOGICAL EVALUATION OF N-ACYL-ANTHRANOYLANTHRANILIC ACID DERIVATIVES AND THEIR CYCLIZED BENZOXAZINONES AS NOVEL HIV-1 NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITORS
inferred← citeshttps://doi.org/10.2174/1568026620666201207095626openalex-snapshot
Docking Paradigm in Drug Design
inferred← citeshttps://doi.org/10.2174/9798898812164125080007openalex-snapshot
Advances in Quantum Mechanical Methods for the Computation of Protein-Ligand Binding Free Energy
inferred← citeshttps://doi.org/10.26686/wgtn.15187563openalex-snapshot
Electrochemical aptasensors: unravelling the critical interactions between aptamers, ligands, and electrodes
inferred← citeshttps://doi.org/10.26686/wgtn.15187563.v1openalex-snapshot
Electrochemical aptasensors: unravelling the critical interactions between aptamers, ligands, and electrodes
inferred← citeshttps://doi.org/10.2741/4527openalex-snapshot
Understanding ligand-receptor non-covalent binding kinetics using molecular modeling
inferred← citeshttps://doi.org/10.3389/fmolb.2023.1210576openalex-snapshot
Solvated interaction energy: from small-molecule to antibody drug design
inferred← citeshttps://doi.org/10.3390/ijms17020144openalex-snapshot
Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods
inferred← citeshttps://doi.org/10.3390/molecules20057700openalex-snapshot
Investigation of Carbohydrate Recognition via Computer Simulation
inferred← citeshttps://doi.org/10.3390/molecules28062731openalex-snapshot
Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors
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