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Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms
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What this work says
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inferred← citeshttps://doi.org/10.1038/s41598-022-11100-3openalex-snapshot
Optimization of IL-1RA structure to achieve a smaller protein with a higher affinity to its receptor
inferred← citeshttps://doi.org/10.1039/c5cp07385eopenalex-snapshot
Biophysical evaluation of protein structural flexibility for ligand biorecognition in solid solution
inferred← citeshttps://doi.org/10.1039/c5ra14661eopenalex-snapshot
In vitro evaluation of the conjugations of neonicotinoids with transport protein: photochemistry, ligand docking and molecular dynamics studies
inferred← citeshttps://doi.org/10.1039/c5sc02678dopenalex-snapshot
Accurate calculation of the absolute free energy of binding for drug molecules
inferred← citeshttps://doi.org/10.1039/c6sc04647aopenalex-snapshot
Investigating allosteric effects on the functional dynamics of β2-adrenergic ternary complexes with enhanced-sampling simulations
inferred← citeshttps://doi.org/10.1039/d1cp00611hopenalex-snapshot
Computational predictions of metal–macrocycle stability constants require accurate treatments of local solvent and pH effects
inferred← citeshttps://doi.org/10.1039/d1md00192bopenalex-snapshot
New perspectives in cancer drug development: computational advances with an eye to design
inferred← citeshttps://doi.org/10.1039/d3nr00397copenalex-snapshot
Metadynamics simulations for the investigation of drug loading on functionalized inorganic nanoparticles
inferred← citeshttps://doi.org/10.1039/d4cp04309jopenalex-snapshot
Navigating the evolution of two-dimensional carbon nitride research: integrating machine learning into conventional approaches
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Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells
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TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules
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Enhanced Sampling Based on Collective Variables
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Molecular dynamics simulation of bioactive compounds of Withania somnifera leaf extract as DNA gyrase inhibitor
inferred← citeshttps://doi.org/10.1080/07391102.2022.2057361openalex-snapshot
Identification of potential Staphylococcus aureus dihydrofolate reductase inhibitors using QSAR, molecular docking, dynamics simulations and free energy calculation
inferred← citeshttps://doi.org/10.1080/17460441.2018.1403419openalex-snapshot
Molecular dynamics simulations and novel drug discovery
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Binding affinity in drug design: experimental and computational techniques
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Pseudoirreversible inhibition elicits persistent efficacy of a sphigosine-1-phosphate receptor-1 antagonist
inferred← citeshttps://doi.org/10.1101/510255openalex-snapshot
Structure-Unbinding Kinetics Relationship of p38α MAPK Inhibitors
inferred← citeshttps://doi.org/10.1146/annurev-physchem-040215-112229openalex-snapshot
Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint
inferred← citeshttps://doi.org/10.1186/s12859-020-03881-zopenalex-snapshot
Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004578openalex-snapshot
Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004619openalex-snapshot
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
inferred← citeshttps://doi.org/10.1371/journal.pone.0143752openalex-snapshot
Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins
inferred← citeshttps://doi.org/10.1371/journal.pone.0207899openalex-snapshot
Conformational sampling of CpxA: Connecting HAMP motions to the histidine kinase function
inferred← citeshttps://doi.org/10.1371/journal.pone.0304451openalex-snapshot
Analysis of AlphaFold and molecular dynamics structure predictions of mutations in serpins
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Flexible receptor docking for drug discovery
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Metadynamics and Free-Energy Landscape Approaches for Structural Characterization of Galectin-3
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-llhdqopenalex-snapshot
A Computational Workflow for Refining AF2 Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive human Adenosine A3 Receptor
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-mc1gwopenalex-snapshot
A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-mvrnjopenalex-snapshot
Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors
inferred← citeshttps://doi.org/10.26434/chemrxiv.11833470.v2openalex-snapshot
A Virtual Reality Ensemble Molecular Dynamics Workflow to Study Complex Conformational Changes in Proteins
inferred← citeshttps://doi.org/10.26434/chemrxiv.14610261openalex-snapshot
APP-C31 Is an Intracellular Promoter of Amyloid-Beta Aggregation and Toxicity
inferred← citeshttps://doi.org/10.26434/chemrxiv.14610261.v1openalex-snapshot
APP-C31 Is an Intracellular Promoter of Amyloid-Beta Aggregation and Toxicity
inferred← citeshttps://doi.org/10.2741/4527openalex-snapshot
Understanding ligand-receptor non-covalent binding kinetics using molecular modeling
inferred← citeshttps://doi.org/10.32657/10356/74803openalex-snapshot
Developing protein force fields for implicit solvent simulation
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Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]
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Computational Insight Into the Small Molecule Intervening PD-L1 Dimerization and the Potential Structure-Activity Relationship
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Exploring the Binding Mechanism of a Supramolecular Tweezer CLR01 to 14-3-3σ Protein via Well-Tempered Metadynamics
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Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes
inferred← citeshttps://doi.org/10.3390/cells8040316openalex-snapshot
Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer
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Recent Trends and Applications of Molecular Modeling in GPCR–Ligand Recognition and Structure-Based Drug Design
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How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs
inferred← citeshttps://doi.org/10.3390/ijms26010167openalex-snapshot
Exploring the Binding Mechanism of ADGRG2 Through Metadynamics and Biochemical Analysis
inferred← citeshttps://doi.org/10.3390/ijms26146780openalex-snapshot
Multistage Molecular Simulations, Design, Synthesis, and Anticonvulsant Evaluation of 2-(Isoindolin-2-yl) Esters of Aromatic Amino Acids Targeting GABAA Receptors via π-π Stacking
inferred← citeshttps://doi.org/10.3390/ijms27156624openalex-snapshot
Flavonoids as Structural Probes Reveal Conformationally Dependent Ligand Recognition in the SARS-CoV-2 JN.1 Spike Protein
inferred← citeshttps://doi.org/10.3390/molecules25071756openalex-snapshot
How Computational Chemistry and Drug Delivery Techniques Can Support the Development of New Anticancer Drugs
inferred← citeshttps://doi.org/10.3390/ph16030376openalex-snapshot
Template Entrance Channel as Possible Allosteric Inhibition and Resistance Site for Quinolines Tricyclic Derivatives in RNA Dependent RNA Polymerase of Bovine Viral Diarrhea Virus
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Role of Artificial Intelligence and Machine Learning in Drug Discovery and Drug Repurposing
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Role of Artificial Intelligence and Machine Learning in Drug Discovery and Drug Repurposing
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Alchemical Response Parameters from an Analytical Model of Molecular Binding
inferred← citeshttps://doi.org/10.48730/ke77-4m21openalex-snapshot
Silk : a biopolymer for engineering nanoparticles
inferred← citeshttps://doi.org/10.5772/intechopen.74939openalex-snapshot
Modeling Soft Supramolecular Nanostructures by Molecular Simulations
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Additional file 1 of Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm
inferred← citeshttps://doi.org/10.70675/7bce36a3zf761z41b4z8daaz3e5e7740dc71openalex-snapshot
Development of predictive approaches for biomolecular association kinetics
inferred← citeshttps://doi.org/10.70675/c050b2bbzdb11z4a27zbdcdzea50700fbb44openalex-snapshot
Coarse-Grained Simulations and Biological Evaluations of Polymer Nanoparticles for Drug Encapsulation and Controlled Release
inferred← citeshttps://doi.org/10.7554/elife.46170openalex-snapshot
Trans-toxin ion-sensitivity of charybdotoxin-blocked potassium-channels reveals unbinding transitional states
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