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Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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A computational study on the role of water and conformational fluctuations in Hsp90 in response to inhibitors
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Mapping putative allosteric sites in rhodopsin and elucidating the structural basis of retigabine modulation
inferred← citeshttps://doi.org/10.1016/j.jtbi.2008.07.030openalex-snapshot
Molecular dynamic simulations analysis of ritronavir and lopinavir as SARS-CoV 3CLpro inhibitors
inferred← citeshttps://doi.org/10.1016/j.jtbi.2013.05.014openalex-snapshot
Extra precision docking, free energy calculation and molecular dynamics simulation studies of CDK2 inhibitors
inferred← citeshttps://doi.org/10.1016/j.molstruc.2014.03.008openalex-snapshot
Combined molecular docking, molecular dynamics simulation and quantitative structure–activity relationship study of pyrimido[1,2-c][1,3]benzothiazin-6-imine derivatives as potent anti-HIV drugs
inferred← citeshttps://doi.org/10.1016/j.neuron.2018.08.011openalex-snapshot
Molecular Dynamics Simulation for All
inferred← citeshttps://doi.org/10.1016/j.phymed.2023.154706openalex-snapshot
Systematic investigation of the multi-scale mechanisms of herbal medicine on treating ventricular remodeling: Theoretical and experimental studies
inferred← citeshttps://doi.org/10.1016/j.phymed.2025.156809openalex-snapshot
Multiscale insights into cornusideʼs effects on NAFLD: A cross-disciplinary integrating bioinformatics, computational chemistry, and machine learning
inferred← citeshttps://doi.org/10.1016/j.redox.2020.101744openalex-snapshot
Resolving the paradox of ferroptotic cell death: Ferrostatin-1 binds to 15LOX/PEBP1 complex, suppresses generation of peroxidized ETE-PE, and protects against ferroptosis
inferred← citeshttps://doi.org/10.1016/j.str.2012.03.009openalex-snapshot
Recognizing Protein-Ligand Binding Sites by Global Structural Alignment and Local Geometry Refinement
inferred← citeshttps://doi.org/10.1016/s0022-2836(03)00289-4openalex-snapshot
Antiviral Inhibition of the HIV-1 Capsid Protein
inferred← citeshttps://doi.org/10.1016/s0065-3233(03)66003-1openalex-snapshot
Protein Simulation and Drug Design
inferred← citeshttps://doi.org/10.1016/s1574-1400(05)01009-1openalex-snapshot
Chapter 9 Calculating Binding Free Energy in Protein–Ligand Interaction
inferred← citeshttps://doi.org/10.1017/cbo9781139021500.024openalex-snapshot
Basic Principles and Practices of Computer-Aided Drug Design
inferred← citeshttps://doi.org/10.1017/s0033583510000284openalex-snapshot
Biomolecular modeling and simulation: a field coming of age
inferred← citeshttps://doi.org/10.1017/s0033583512000066openalex-snapshot
Protein flexibility in docking and surface mapping
inferred← citeshttps://doi.org/10.1021/acs.biochem.5b00018openalex-snapshot
Multiple Drug Transport Pathways through Human P-Glycoprotein
inferred← citeshttps://doi.org/10.1021/acs.jafc.6b01067openalex-snapshot
Computational Study Exploring the Interaction Mechanism of Benzimidazole Derivatives as Potent Cattle Bovine Viral Diarrhea Virus Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00452openalex-snapshot
Discovery of Novel Small-Molecule Calcium Sensitizers for Cardiac Troponin C: A Combined Virtual and Experimental Screening Approach
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00848openalex-snapshot
Actives-Based Receptor Selection Strongly Increases the Success Rate in Structure-Based Drug Design and Leads to Identification of 22 Potent Cancer Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01531openalex-snapshot
Activity Models of Key GPCR Families in the Central Nervous System: A Tool for Many Purposes
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00416openalex-snapshot
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00169openalex-snapshot
A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00484openalex-snapshot
Ensemble-Based Virtual Screening Led to the Discovery of New Classes of Potent Tyrosinase Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00125openalex-snapshot
Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00439openalex-snapshot
Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00536openalex-snapshot
Successful Identification of Cardiac Troponin Calcium Sensitizers Using a Combination of Virtual Screening and ROC Analysis of Known Troponin C Binders
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00314openalex-snapshot
Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00730openalex-snapshot
Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00905openalex-snapshot
Highly Flexible Ligand Docking: Benchmarking of the DockThor Program on the LEADS-PEP Protein–Peptide Data Set
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c01177openalex-snapshot
Accelerated Ligand-Mapping Molecular Dynamics Simulations for the Detection of Recalcitrant Cryptic Pockets and Occluded Binding Sites
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00478openalex-snapshot
Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00653openalex-snapshot
A Robust Induced Fit Docking Approach with the Combination of the Hybrid All-Atom/United-Atom/Coarse-Grained Model and Simulated Annealing
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b01684openalex-snapshot
Role of Molecular Dynamics and Related Methods in Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jpclett.1c01064openalex-snapshot
Mechanism of Ligand Recognition by Human ACE2 Receptor
inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.7b00505openalex-snapshot
Systems Pharmacology Dissection of Multiscale Mechanisms of Action for Herbal Medicines in Treating Rheumatoid Arthritis
inferred← citeshttps://doi.org/10.1021/acschemneuro.6b00216openalex-snapshot
Multistep Modeling Strategy To Improve the Binding Affinity Prediction of PET Tracers to Aβ42: Case Study with Styrylbenzoxazole Derivatives
inferred← citeshttps://doi.org/10.1021/acsomega.3c01314openalex-snapshot
Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro , and X-ray Crystallography
inferred← citeshttps://doi.org/10.1021/acsomega.5c00981openalex-snapshot
AI-Driven Multiscale Study on the Mechanism of Polygonati Rhizoma in Regulating Immune Function in STAD
inferred← citeshttps://doi.org/10.1021/bi2004558openalex-snapshot
Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations
inferred← citeshttps://doi.org/10.1021/bi300299zopenalex-snapshot
Catalytic Transitions in the Human MDR1 P-Glycoprotein Drug Binding Sites
inferred← citeshttps://doi.org/10.1021/bi301358aopenalex-snapshot
Ligand Access to the Active Site in Thermus thermophilusba3 and Bovine Heart aa3 Cytochrome Oxidases
inferred← citeshttps://doi.org/10.1021/bi500490zopenalex-snapshot
Molecular Mechanism of Viral Resistance to a Potent Non-nucleoside Inhibitor Unveiled by Molecular Simulations
inferred← citeshttps://doi.org/10.1021/bi700253qopenalex-snapshot
Simulated Interactions between Angiotensin-Converting Enzyme and Substrate Gonadotropin-Releasing Hormone: Novel Insights into Domain Selectivity
inferred← citeshttps://doi.org/10.1021/ci1001857openalex-snapshot
Exploring the Binding Site of C-Terminal Hsp90 Inhibitors
inferred← citeshttps://doi.org/10.1021/ci100457topenalex-snapshot
Significant Enhancement of Docking Sensitivity Using Implicit Ligand Sampling
inferred← citeshttps://doi.org/10.1021/ci100461kopenalex-snapshot
A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins
inferred← citeshttps://doi.org/10.1021/ci200112bopenalex-snapshot
Long-Range Effects of a Peripheral Mutation on the Enzymatic Activity of Cytochrome P450 1A2
inferred← citeshttps://doi.org/10.1021/ci200117nopenalex-snapshot
Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci2001742openalex-snapshot
Accurate Prediction of the Bound Form of the Akt Pleckstrin Homology Domain Using Normal Mode Analysis To Explore Structural Flexibility
inferred← citeshttps://doi.org/10.1021/ci200220vopenalex-snapshot
Robust Scoring Functions for Protein–Ligand Interactions with Quantum Chemical Charge Models
inferred← citeshttps://doi.org/10.1021/ci2002878openalex-snapshot
Combined 3D-QSAR, Molecular Docking, and Molecular Dynamics Study on Piperazinyl-Glutamate-Pyridines/Pyrimidines as Potent P2Y12 Antagonists for Inhibition of Platelet Aggregation
inferred← citeshttps://doi.org/10.1021/ci200428topenalex-snapshot
Utilizing Experimental Data for Reducing Ensemble Size in Flexible-Protein Docking
inferred← citeshttps://doi.org/10.1021/ci2005934openalex-snapshot
Potential and Limitations of Ensemble Docking
inferred← citeshttps://doi.org/10.1021/ci300040copenalex-snapshot
Novel Inhibitor Discovery through Virtual Screening against Multiple Protein Conformations Generated via Ligand-Directed Modeling: A Maternal Embryonic Leucine Zipper Kinase Example
inferred← citeshttps://doi.org/10.1021/ci300326dopenalex-snapshot
An Automated Docking Protocol for hERG Channel Blockers
inferred← citeshttps://doi.org/10.1021/ci300432wopenalex-snapshot
Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design
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