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Target Flexibility: An Emerging Consideration in Drug Discovery and Design
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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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Ensemble-docking approach on BACE-1: Pharmacophore Perception and Directives for Drug Development
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FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function
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Scalable molecular dynamics with NAMD
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Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
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Flexible relaxation of rigid‐body docking solutions
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FLIPDock: Docking flexible ligands into flexible receptors
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Automated docking of substrates to proteins by simulated annealing
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Molecular docking to ensembles of protein structures 1 1Edited by B. Honig
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FlexE: efficient molecular docking considering protein structure variations
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Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
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Strategies for the design of inhibitors of aldose reductase, an enzyme showing pronounced induced-fit adaptations
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Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
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Computer-aided drug design: the next 20 years
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Improving database enrichment through ensemble docking
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A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
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A geometric approach to macromolecule-ligand interactions
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The crystal structure of human deoxyhaemoglobin at 1.74 Å resolution
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Mapping protein dynamics by X-ray diffraction
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Stability improvement of the fatty acid binding protein Sm14 from S. mansoni by Cys replacement: Structural and functional characterization of a vaccine candidate
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Scoring functions for protein–ligand interactions: a critical perspective
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Consensus scoring for protein–ligand interactions
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The consequences of scoring docked ligand conformations using free energy correlations
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Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
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Testing a Flexible-receptor Docking Algorithm in a Model Binding Site
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Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding
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High-resolution Crystal Structure of Aldose Reductase Complexed with the Novel Sulfonyl-pyridazinone Inhibitor Exhibiting an Alternative Active Site Anchoring Group
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Expect the Unexpected or Caveat for Drug Designers: Multiple Structure Determinations Using Aldose Reductase Crystals Treated under Varying Soaking and Co-crystallisation Conditions
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How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding
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Lipids, lipid rafts and caveolae: Their importance for GPCR signaling and their centrality to the endocannabinoid system
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Advances in kinetic protein crystallography
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Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
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Flexible ligand docking to multiple receptor conformations: a practical alternative
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Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus
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The native-state ensemble of proteins provides clues for folding, misfolding and function
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Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model
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Efficient Conformational Sampling of Local Side-chain Flexibility
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Statistical Thermodynamic Linkage Between Conformational And Binding Equilibria
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[18] Refinement and reliability of macromolecular models based on X-ray diffraction data
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G protein-coupled receptor interacting proteins: Emerging roles in localization and signal transduction
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Statistical potentials and scoring functions applied to protein–ligand binding
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New structures of allosteric proteins revealing remarkable conformational changes
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Intrinsically unstructured proteins
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Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
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Protein flexibility as revealed by fluorescence resonance energy transfer: an extension of the method for systems with multiple labels
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Transcriptional Repression by Nuclear Hormone Receptors
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Consensus scoring for ligand/protein interactions
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Identifying protein folding cores from the evolution of flexible regions during unfolding
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A Chemical, Genetic, and Structural Analysis of the Nuclear Bile Acid Receptor FXR
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Structural Basis for Bile Acid Binding and Activation of the Nuclear Receptor FXR
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A Covalent Modification of NADP+ Revealed by the Atomic Resolution Structure of FprA, a Mycobacterium tuberculosis Oxidoreductase,
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The Enigma of the Liganded Hemoglobin End State: A Novel Quaternary Structure of Human Carbonmonoxy Hemoglobin,
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Gα-Subunits Differentially Alter the Conformation and Agonist Affinity of κ-Opioid Receptors
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Molecular Dynamics Simulations of the Ligand-Induced Chemical Information Transfer in the 5-HT1AReceptor
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GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein−Ligand Complexes
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Structure-Based Virtual Screening with Supervised Consensus Scoring: Evaluation of Pose Prediction and Enrichment Factors
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Computational Modeling Approaches to Structure−Function Analysis of G Protein-Coupled Receptors
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Interpretation of atomic displacement parameters from diffraction studies of crystals
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Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme
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Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes
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Computational Titration Analysis of a Multiprotic HIV-1 Protease−Ligand Complex
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Incorporating Protein Flexibility in Structure-Based Drug Discovery: Using HIV-1 Protease as a Test Case
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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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Development of a Quantum Mechanics-Based Free-Energy Perturbation Method: Use in the Calculation of Relative Solvation Free Energies
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Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design
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Relative Binding Affinities of Fructose-1,6-Bisphosphatase Inhibitors Calculated Using a Quantum Mechanics-Based Free Energy Perturbation Method
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Mechanisms of Inter- and Intramolecular Communication in GPCRs and G Proteins
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Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
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Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 2. Computational Titration and pH Effects in Molecular Models of Neuraminidase−Inhibitor Complexes
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Discovery of a Novel Binding Trench in HIV Integrase
inferredcites →https://doi.org/10.1021/jm050075jopenalex-snapshot
“In Situ Cross-Docking” To Simultaneously Address Multiple Targets
inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
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Naphtho[1,2-d]isothiazole Acetic Acid Derivatives as a Novel Class of Selective Aldose Reductase Inhibitors
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Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
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Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
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Dissection of the Recognition Properties of p38 MAP Kinase. Determination of the Binding Mode of a New Pyridinyl−Heterocycle Inhibitor Family
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A Flexible Approach to Induced Fit Docking
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Determination of Protein–Ligand Binding Modes Using Complexation-Induced Changes in 1H NMR Chemical Shift
inferredcites →https://doi.org/10.1021/jp0356158openalex-snapshot
pKa Calculations with QM/MM Free Energy Perturbations
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Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes
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Towards Accurate Ab Initio QM/MM Calculations of Free-Energy Profiles of Enzymatic Reactions
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Virtual screening with solvation and ligand-induced complementarity
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Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
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NMR studies of structure and function of biological macromolecules (Nobel Lecture)*
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Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling
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Letter to the Editor: 1H, 15N and 13C resonance assignments of the apo Sm14-M20(C62V) protein, a mutant of Schistosoma mansoni Sm14
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A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis
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Three Dimensional Fourier Synthesis of Horse Deoxyhaemoglobin at 2.8 Å Resolution
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Identifying conformational changes with site-directed spin labeling.
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Intrinsic dynamics of an enzyme underlies catalysis
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Crystal structure of the human β2 adrenergic G-protein-coupled receptor
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A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
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Dynamic personalities of proteins
inferredcites →https://doi.org/10.1038/nbt999openalex-snapshot
Ligand selectivity and competition between enzymes in silico
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Docking and scoring in virtual screening for drug discovery: methods and applications
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Efficacy at g-protein-coupled receptors
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Studying excited states of proteins by NMR spectroscopy.
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Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair
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Roles of G‐protein‐coupled receptor dimerization
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Proton–proton Overhauser NMR spectroscopy with polypeptide chains in large structures
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Crystal structure of a photoactivated deprotonated intermediate of rhodopsin
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Ligand configurational entropy and protein binding
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Structure of outer membrane protein G by solution NMR spectroscopy
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Binding of small molecules to an adaptive protein–protein interface
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Gene Structure and M20T Polymorphism of theSchistosoma mansoni Sm14 Fatty Acid-binding Protein
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Constrained geometric simulation of diffusive motion in proteins
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Folding funnels and binding mechanisms
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Expanding the model: anisotropic displacement parameters in protein structure refinement
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Side‐chain flexibility in protein–ligand binding: The minimal rotation hypothesis
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Folding funnels, binding funnels, and protein function
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Ion channels: their structure, function and control – an overview
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Raman-Assisted Crystallography Reveals End-On Peroxide Intermediates in a Nonheme Iron Enzyme
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High-Resolution Crystal Structure of an Engineered Human β 2 -Adrenergic G Protein–Coupled Receptor
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G Protein–Coupled Receptor Rhodopsin
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WHATEVER HAPPENED TO THE FUN? An Autobiographical Investigation
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Small-Angle X-Ray Scattering from RNA, Proteins, and Protein Complexes
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An Intracellular Loop (IL2) Residue Confers Different Basal Constitutive Activities to the Human Lutropin Receptor and Human Thyrotropin Receptor through Structural Communication between IL2 and Helix 6, via Helix 3
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Crucial Role of the H11-H12 Loop in Stabilizing the Active Conformation of the Human Mineralocorticoid Receptor
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Contributions of Intracellular Loops 2 and 3 of the Lutropin Receptor in Gs Coupling
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Protein-Ligand Interaction Probed by Time-Resolved Crystallography
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Incorporating protein flexibility into docking and structure-based drug design
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Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design
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HIV Integrase Inhibitors: From Diketoacids to Heterocyclic Templates: A History of HIV Integrase Medicinal Chemistry at Merck West Point and Merck Rome (IRBM)
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Scoring Functions for Virtual Screening
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The stereochemistry of the protein myoglobin
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A novel quaternary structure of human carbonmonoxy hemoglobin
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Using AutoDock for Ligand‐Receptor Docking
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Receptor Targets in Drug Discovery
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Docking and Scoring in Drug Discovery
inferred← citeshttps://doi.org/10.1002/0471266949.bmc148openalex-snapshot
Protein Flexibility in In Silico Screening
inferred← citeshttps://doi.org/10.1002/0471266949.bmc301openalex-snapshot
Docking, Scoring, and Virtual Screening in Drug Discovery
inferred← citeshttps://doi.org/10.1002/9781118523063.ch8openalex-snapshot
Virtual Ligand Screening Against Comparative Models of Proteins
inferred← citeshttps://doi.org/10.1002/9781118681121.ch22openalex-snapshot
Integrating Evolution of Drug Resistance into Drug Discovery
inferred← citeshttps://doi.org/10.1002/9781119945888.ch8openalex-snapshot
Halogen…π Interactions as Important Contributors to Binding Affinity in Medicinal Chemistry
inferred← citeshttps://doi.org/10.1002/9783527633326.ch15openalex-snapshot
Target‐Based Virtual Screening on Small‐Molecule Protein Binding Sites
inferred← citeshttps://doi.org/10.1002/9783527633326.ch16openalex-snapshot
Target‐Based Virtual Screening to Address Protein–Protein Interfaces
inferred← citeshttps://doi.org/10.1002/9783527633326.ch7openalex-snapshot
The Challenge of Affinity Prediction: Scoring Functions for Structure‐Based Virtual Screening
inferred← citeshttps://doi.org/10.1002/9783527633326.ch8openalex-snapshot
Protein Flexibility in Structure‐Based Virtual Screening: From Models to Algorithms
inferred← citeshttps://doi.org/10.1002/9783527633326.ch9openalex-snapshot
Handling Protein Flexibility in Docking and High‐Throughput Docking: From Algorithms to Applications
inferred← citeshttps://doi.org/10.1002/9783527636402.ch18openalex-snapshot
Statics of Biomacromolecules
inferred← citeshttps://doi.org/10.1002/9783527645947.ch11openalex-snapshot
Free Energy Calculations in Drug Lead Optimization
inferred← citeshttps://doi.org/10.1002/9783527645947.ch14openalex-snapshot
Embracing Protein Plasticity in Ligand Docking
inferred← citeshttps://doi.org/10.1002/9783527645947.ch9openalex-snapshot
Implicit Solvent Models and Electrostatics in Molecular Recognition
inferred← citeshttps://doi.org/10.1002/ange.201205676openalex-snapshot
Using Ligand‐Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo‐Like Kinase 1
inferred← citeshttps://doi.org/10.1002/anie.201205676openalex-snapshot
Using Ligand‐Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo‐Like Kinase 1
inferred← citeshttps://doi.org/10.1002/chin.200903235openalex-snapshot
ChemInform Abstract: Target Flexibility: An Emerging Consideration in Drug Discovery and Design
inferred← citeshttps://doi.org/10.1002/cmdc.200800301openalex-snapshot
Virtual Screening and Biological Characterization of Novel Histone Arginine Methyltransferase PRMT1 Inhibitors
inferred← citeshttps://doi.org/10.1002/cmdc.200900373openalex-snapshot
Discovery of Potent Vascular Endothelial Growth Factor Receptor‐2 Inhibitors
inferred← citeshttps://doi.org/10.1002/cmdc.201200508openalex-snapshot
Discovery of Schaeffer’s Acid Analogues as Lead Structures of Mycobacterium tuberculosis Type II Dehydroquinase Using a Rational Drug Design Approach
inferred← citeshttps://doi.org/10.1002/ddr.20399openalex-snapshot
Role of protein flexibility in the discovery of new drugs
inferred← citeshttps://doi.org/10.1002/jcc.21251openalex-snapshot
Insights into docking and scoring neuronal α4β2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations
inferred← citeshttps://doi.org/10.1002/jcc.21306openalex-snapshot
Drug efficiency indices for improvement of molecular docking scoring functions
inferred← citeshttps://doi.org/10.1002/jcc.21601openalex-snapshot
Predicting the accuracy of protein–ligand docking on homology models
inferred← citeshttps://doi.org/10.1002/jcc.23026openalex-snapshot
Balancing target flexibility and target denaturation in computational fragment‐based inhibitor discovery
inferred← citeshttps://doi.org/10.1002/jcc.23680openalex-snapshot
Including ligand‐induced protein flexibility into protein tunnel prediction
inferred← citeshttps://doi.org/10.1002/jcc.24259openalex-snapshot
Flexible CDOCKER : Development and application of a pseudo‐explicit structure‐based docking method within CHARMM
inferred← citeshttps://doi.org/10.1002/med.20241openalex-snapshot
HIV‐1 NNRTIs: structural diversity, pharmacophore similarity, and impliations for drug design
inferred← citeshttps://doi.org/10.1002/minf.200900078openalex-snapshot
In Pursuit of Fully Flexible Protein‐Ligand Docking: Modeling the Bilateral Mechanism of Binding
inferred← citeshttps://doi.org/10.1002/minf.201000017openalex-snapshot
Impact of the Recent Mouse P‐Glycoprotein Structure for Structure‐Based Ligand Design
inferred← citeshttps://doi.org/10.1002/minf.201000162openalex-snapshot
Addressing the Conformational Flexibility of Serine Racemase by Combining Targeted Molecular Dynamics, Conformational Sampling and Docking Studies
inferred← citeshttps://doi.org/10.1002/minf.201300082openalex-snapshot
Identification of Similar Binding Sites to Detect Distant Polypharmacology
inferred← citeshttps://doi.org/10.1002/minf.202000148openalex-snapshot
Dynamic‐shared Pharmacophore Approach as Tool to Design New Allosteric PRC2 Inhibitors, Targeting EED Binding Pocket
inferred← citeshttps://doi.org/10.1002/pro.132openalex-snapshot
Relating protein conformational changes to packing efficiency and disorder
inferred← citeshttps://doi.org/10.1002/pro.192openalex-snapshot
Blind docking of pharmaceutically relevant compounds using RosettaLigand
inferred← citeshttps://doi.org/10.1002/pro.366openalex-snapshot
A flexible docking scheme to explore the binding selectivity of PDZ domains
inferred← citeshttps://doi.org/10.1002/pro.38openalex-snapshot
StoneHinge: Hinge prediction by network analysis of individual protein structures
inferred← citeshttps://doi.org/10.1002/prot.22537openalex-snapshot
Modeling the possible conformations of the extracellular loops in G‐protein‐coupled receptors
inferred← citeshttps://doi.org/10.1002/prot.22629openalex-snapshot
DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility
inferred← citeshttps://doi.org/10.1002/prot.22826openalex-snapshot
Flexibility and inhibitor binding in cdc25 phosphatases
inferred← citeshttps://doi.org/10.1002/qua.25678openalex-snapshot
Computational chemistry in drug lead discovery and design
inferred← citeshttps://doi.org/10.1002/slct.202101801openalex-snapshot
Exploring Ruthenium‐Based Organometallic Inhibitors against Plasmodium falciparum Calcium Dependent Kinase 2 (PfCDPK2): A Combined Ensemble Docking, QM/MM and Molecular Dynamics Study
inferred← citeshttps://doi.org/10.1002/wcms.1311openalex-snapshot
Rigidity theory for biomolecules: concepts, software, and applications
inferred← citeshttps://doi.org/10.1002/wcms.1320openalex-snapshot
Recent advances in dynamic docking for drug discovery
inferred← citeshttps://doi.org/10.1002/wcms.1367openalex-snapshot
Computational structure‐based drug design: Predicting target flexibility
inferred← citeshttps://doi.org/10.1002/wcms.1544openalex-snapshot
Structure based virtual screening: Fast and slow
inferred← citeshttps://doi.org/10.1002/wcms.18openalex-snapshot
Outstanding challenges in protein–ligand docking and structure‐based virtual screening
inferred← citeshttps://doi.org/10.1002/wcms.29openalex-snapshot
Receptor flexibility in small‐molecule docking calculations
inferred← citeshttps://doi.org/10.1002/wcms.69openalex-snapshot
Two personal perspectives on a key issue in contemporary 3D QSAR
inferred← citeshttps://doi.org/10.1002/widm.46openalex-snapshot
Mining flexible‐receptor molecular docking data
inferred← citeshttps://doi.org/10.1007/164_2021_515openalex-snapshot
The Application of In Silico Methods on Umami Taste Receptor
inferred← citeshttps://doi.org/10.1007/978-1-0716-0282-9_17openalex-snapshot
Molecular Docking Using Quantum Mechanical-Based Methods
inferred← citeshttps://doi.org/10.1007/978-1-4614-2146-7_4openalex-snapshot
Small Molecule Docking from Theoretical Structural Models
inferred← citeshttps://doi.org/10.1007/978-1-4939-1465-4_20openalex-snapshot
Molecular Docking to Flexible Targets
inferred← citeshttps://doi.org/10.1007/978-1-4939-7404-7_19openalex-snapshot
Computational Modeling of Multi-target-Directed Inhibitors Against Alzheimer’s Disease
inferred← citeshttps://doi.org/10.1007/978-1-4939-7404-7_3openalex-snapshot
Computer-Aided Drug Design Approaches to Study Key Therapeutic Targets in Alzheimer’s Disease
inferred← citeshttps://doi.org/10.1007/978-1-61779-465-0_1openalex-snapshot
A Molecular Dynamics Ensemble-Based Approach for the Mapping of Druggable Binding Sites
inferred← citeshttps://doi.org/10.1007/978-1-61779-465-0_11openalex-snapshot
Normal Mode-Based Approaches in Receptor Ensemble Docking
inferred← citeshttps://doi.org/10.1007/978-1-61779-465-0_6openalex-snapshot
Flexibility Analysis of Biomacromolecules with Application to Computer-Aided Drug Design
inferred← citeshttps://doi.org/10.1007/978-1-62703-658-0_10openalex-snapshot
Geometric Simulation of Flexible Motion in Proteins
inferred← citeshttps://doi.org/10.1007/978-3-030-18375-2_11openalex-snapshot
Molecular Modeling and Drug Design Techniques in Microbial Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-3-030-78315-0_12openalex-snapshot
Computational Applications on Food Contact Chemicals as Nuclear Receptor Binders
inferred← citeshttps://doi.org/10.1007/978-3-642-03223-3_13openalex-snapshot
FReDD: Supporting Mining Strategies through a Flexible-Receptor Docking Database
inferred← citeshttps://doi.org/10.1007/978-3-642-16712-6_122openalex-snapshot
Terahertz Spectroscopy: Protein Dynamics
inferred← citeshttps://doi.org/10.1007/978-3-642-32639-4_82openalex-snapshot
Improving Differential Evolution Accuracy for Flexible Ligand Docking Using a Multi-solution Strategy
inferred← citeshttps://doi.org/10.1007/978-90-481-3034-4_16openalex-snapshot
Challenges for Computer Simulations in Drug Design
inferred← citeshttps://doi.org/10.1007/978-94-017-9257-8_15openalex-snapshot
(How to) Profit from Molecular Dynamics-based Ensemble Docking
inferred← citeshttps://doi.org/10.1007/978-981-97-0814-7_10openalex-snapshot
Bioinformatics and Computational Biology
inferred← citeshttps://doi.org/10.1007/s00204-020-02897-xopenalex-snapshot
Virtual screening of potentially endocrine-disrupting chemicals against nuclear receptors and its application to identify PPARγ-bound fatty acids
inferred← citeshttps://doi.org/10.1007/s00249-010-0592-0openalex-snapshot
How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis
inferred← citeshttps://doi.org/10.1007/s00706-009-0220-9openalex-snapshot
Derivatives of 5-nitro-1H-benzo[de]isoquinoline-1,3(2H)-dione: design, synthesis, and biological activity
inferred← citeshttps://doi.org/10.1007/s00894-015-2826-7openalex-snapshot
Ligand similarity guided receptor selection enhances docking accuracy and recall for non-nucleoside HIV reverse transcriptase inhibitors
inferred← citeshttps://doi.org/10.1007/s10822-010-9363-3openalex-snapshot
Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
inferred← citeshttps://doi.org/10.1007/s10822-011-9415-3openalex-snapshot
Molecular motions in drug design: the coming age of the metadynamics method
inferred← citeshttps://doi.org/10.1007/s10822-011-9453-xopenalex-snapshot
Free energy calculations offer insights into the influence of receptor flexibility on ligand–receptor binding affinities
inferred← citeshttps://doi.org/10.1007/s10822-011-9504-3openalex-snapshot
Lions and tigers and bears, oh my! Three barriers to progress in computer-aided molecular design
inferred← citeshttps://doi.org/10.1007/s10822-012-9578-6openalex-snapshot
Multiple ligand docking by Glide: implications for virtual second-site screening
inferred← citeshttps://doi.org/10.1007/s10822-014-9728-0openalex-snapshot
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling
inferred← citeshttps://doi.org/10.1007/s10822-016-9979-zopenalex-snapshot
Docking-undocking combination applied to the D3R Grand Challenge 2015
inferred← citeshttps://doi.org/10.1007/s10822-018-0100-7openalex-snapshot
Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control
inferred← citeshttps://doi.org/10.1007/s10822-020-00294-1openalex-snapshot
SAMPL6 host–guest binding affinities and binding poses from spherical-coordinates-biased simulations
inferred← citeshttps://doi.org/10.1007/s10822-020-00335-9openalex-snapshot
SAMPL7 TrimerTrip host–guest binding poses and binding affinities from spherical-coordinates-biased simulations
inferred← citeshttps://doi.org/10.1007/s10822-023-00527-zopenalex-snapshot
ChemFlow_py: a flexible toolkit for docking and rescoring
inferred← citeshttps://doi.org/10.1007/s10930-021-10031-8openalex-snapshot
Protein–Protein Docking: Past, Present, and Future
inferred← citeshttps://doi.org/10.1007/s11515-011-1125-7openalex-snapshot
Novel computational biology methods and their applications to drug discovery
inferred← citeshttps://doi.org/10.1007/s12038-012-9273-8openalex-snapshot
What in silico molecular docking can do for the ‘bench-working biologists’
inferred← citeshttps://doi.org/10.1016/b978-0-12-407865-9.00014-5openalex-snapshot
Application of Monte Carlo-Based Receptor Ensemble Docking to Virtual Screening for GPCR Ligands
inferred← citeshttps://doi.org/10.1016/b978-0-12-801505-6.00010-7openalex-snapshot
Other Related Techniques
inferred← citeshttps://doi.org/10.1016/b978-0-12-821748-1.00009-9openalex-snapshot
Advances in structure-based drug design
inferred← citeshttps://doi.org/10.1016/bs.apha.2025.02.006openalex-snapshot
Predictive cavity and binding site identification: Techniques and applications
inferred← citeshttps://doi.org/10.1016/bs.armc.2022.08.006openalex-snapshot
No dance, no partner! A tale of receptor flexibility in docking and virtual screening
inferred← citeshttps://doi.org/10.1016/bs.pmbts.2024.03.023openalex-snapshot
Synergizing drug repurposing and target identification for neurodegenerative diseases
inferred← citeshttps://doi.org/10.1016/j.abb.2011.10.009openalex-snapshot
Structural and functional characterization of α-isopropylmalate synthase and citramalate synthase, members of the LeuA dimer superfamily
inferred← citeshttps://doi.org/10.1016/j.abb.2015.08.002openalex-snapshot
Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description
inferred← citeshttps://doi.org/10.1016/j.arabjc.2019.12.006openalex-snapshot
Synthesis, characterization, anticancer activity, and molecular docking of some new sugar hydrazone and arylidene derivatives
inferred← citeshttps://doi.org/10.1016/j.bbagen.2011.06.001openalex-snapshot
Ligand-induced fit affects binding modes and provokes changes in crystal packing of aldose reductase
inferred← citeshttps://doi.org/10.1016/j.bbapap.2010.06.008openalex-snapshot
Analysis of binding modes of ligands to multiple conformations of CYP3A4
inferred← citeshttps://doi.org/10.1016/j.bcp.2010.06.004openalex-snapshot
Temperature dependent photolabeling of the human angiotensin II type 1 receptor reveals insights into its conformational landscape and its activation mechanism
inferred← citeshttps://doi.org/10.1016/j.bioorg.2026.110154openalex-snapshot
Insight into the reactivity and antitumoral potential of allyl rhodanine derivatives: Azomethine ylide cycloadditions, molecular docking, and SAR studies
inferred← citeshttps://doi.org/10.1016/j.bmc.2009.05.035openalex-snapshot
Retinoid receptor subtype-selective modulators through synthetic modifications of RARγ agonists
inferred← citeshttps://doi.org/10.1016/j.bmc.2012.09.024openalex-snapshot
Benzimidazole inhibitors of the protein kinase CHK2: Clarification of the binding mode by flexible side chain docking and protein–ligand crystallography
inferred← citeshttps://doi.org/10.1016/j.bmc.2016.08.010openalex-snapshot
Challenges of docking in large, flexible and promiscuous binding sites
inferred← citeshttps://doi.org/10.1016/j.bmcl.2016.11.019openalex-snapshot
A matrix-focused structure-activity and binding site flexibility study of quinolinol inhibitors of botulinum neurotoxin serotype A
inferred← citeshttps://doi.org/10.1016/j.bpc.2009.04.003openalex-snapshot
The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15N chemical shifts
inferred← citeshttps://doi.org/10.1016/j.bpc.2012.10.005openalex-snapshot
Assessing the chemical accuracy of protein structures via peptide acidity
inferred← citeshttps://doi.org/10.1016/j.bpj.2008.12.3752openalex-snapshot
Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Studied Using Well-Sampled “Semi-Atomistic” Simulations
inferred← citeshttps://doi.org/10.1016/j.cbpa.2010.06.169openalex-snapshot
Intrinsically disordered proteins are potential drug targets
inferred← citeshttps://doi.org/10.1016/j.chembiol.2015.03.019openalex-snapshot
Surface-Induced Dissociation of Homotetramers with D2 Symmetry Yields their Assembly Pathways and Characterizes the Effect of Ligand Binding
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2013.12.003openalex-snapshot
Collective variable driven molecular dynamics to improve protein–protein docking scoring
inferred← citeshttps://doi.org/10.1016/j.cotox.2017.01.011openalex-snapshot
Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms
inferred← citeshttps://doi.org/10.1016/j.csbj.2014.12.002openalex-snapshot
What can we learn from molecular dynamics simulations for GPCR drug design?
inferred← citeshttps://doi.org/10.1016/j.csbr.2025.100067openalex-snapshot
Molecular mechanisms underlying enhanced ACE-2-RBD stability in SARS-CoV-2 variants: The impact of key SARS-CoV-2 RBD mutations
inferred← citeshttps://doi.org/10.1016/j.drudis.2009.01.003openalex-snapshot
Managing protein flexibility in docking and its applications
inferred← citeshttps://doi.org/10.1016/j.drudis.2010.05.015openalex-snapshot
Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery
inferred← citeshttps://doi.org/10.1016/j.drudis.2010.08.003openalex-snapshot
Computational quantum chemistry and adaptive ligand modeling in mechanistic QSAR
inferred← citeshttps://doi.org/10.1016/j.drudis.2013.10.027openalex-snapshot
Modelling three-dimensional protein structures for applications in drug design
inferred← citeshttps://doi.org/10.1016/j.ejmech.2012.01.003openalex-snapshot
A new approach for investigating protein flexibility based on Constraint Logic Programming. The first application in the case of the estrogen receptor
inferred← citeshttps://doi.org/10.1016/j.ejmech.2015.09.024openalex-snapshot
Mutational mapping of the transmembrane binding site of the G-protein coupled receptor TGR5 and binding mode prediction of TGR5 agonists
inferred← citeshttps://doi.org/10.1016/j.ejmech.2018.05.035openalex-snapshot
Discovery of potent and novel smoothened antagonists via structure-based virtual screening and biological assays
inferred← citeshttps://doi.org/10.1016/j.ejps.2022.106324openalex-snapshot
CADD, AI and ML in drug discovery: A comprehensive review
inferred← citeshttps://doi.org/10.1016/j.eswa.2014.05.038openalex-snapshot
A strategic solution to optimize molecular docking simulations using Fully-Flexible Receptor models
inferred← citeshttps://doi.org/10.1016/j.jbiotec.2011.12.005openalex-snapshot
Structure-based computational analysis of protein binding sites for function and druggability prediction
inferred← citeshttps://doi.org/10.1016/j.jmb.2008.11.010openalex-snapshot
RosettaLigand Docking with Full Ligand and Receptor Flexibility
inferred← citeshttps://doi.org/10.1016/j.jmgm.2010.11.005openalex-snapshot
Docking-based virtual screening for ligands of G protein-coupled receptors: Not only crystal structures but also in silico models
inferred← citeshttps://doi.org/10.1016/j.jmgm.2011.09.006openalex-snapshot
Binding of GSH conjugates to π-GST: A cross-docking approach
inferred← citeshttps://doi.org/10.1016/j.jmgm.2018.11.016openalex-snapshot
Molecular modelling and competitive inhibition of a Mycobacterium tuberculosis multidrug-resistance efflux pump
inferred← citeshttps://doi.org/10.1016/j.jmgm.2021.107886openalex-snapshot
Identification of viable TCDD access pathways to human AhR PAS-B ligand binding domain
inferred← citeshttps://doi.org/10.1016/j.jmgm.2026.109423openalex-snapshot
Integrative network pharmacology and molecular simulations reveal the Anti-DKD potential of Pedalium murex phytocompounds via TNF-α and NF-κB inhibition
inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2016.09.010openalex-snapshot
Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses
inferred← citeshttps://doi.org/10.1016/j.pharmthera.2025.108797openalex-snapshot
Conformationally adaptive therapeutic peptides for diseases caused by intrinsically disordered proteins (IDPs). New paradigm for drug discovery: Target the target, not the arrow
inferred← citeshttps://doi.org/10.1016/j.saa.2023.123816openalex-snapshot
An Optimized Purification Protocol for Enzymatically Synthesized S-Adenosyl-L-Methionine (Sam) for Applications in Solution State Infrared Spectroscopic Studies
inferred← citeshttps://doi.org/10.1016/j.sbi.2024.102871openalex-snapshot
Increased throughput in methods for simulating protein ligand binding and unbinding
inferred← citeshttps://doi.org/10.1016/j.str.2009.02.010openalex-snapshot
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
inferred← citeshttps://doi.org/10.1016/j.str.2013.07.012openalex-snapshot
Efficient and Robust Analysis of Biomacromolecular Flexibility Using Ensembles of Network Topologies Based on Fuzzy Noncovalent Constraints
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.10.019openalex-snapshot
Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies
inferred← citeshttps://doi.org/10.1016/s0079-6468(10)49004-9openalex-snapshot
Computational Analysis of Structure–Activity Relationships
inferred← citeshttps://doi.org/10.1017/cbo9781139021500.024openalex-snapshot
Basic Principles and Practices of Computer-Aided Drug Design
inferred← citeshttps://doi.org/10.1017/s0033583512000066openalex-snapshot
Protein flexibility in docking and surface mapping
inferred← citeshttps://doi.org/10.1021/acs.biomac.2c00652openalex-snapshot
Recognition of a Flexible Protein Loop in Taspase 1 by Multivalent Supramolecular Tweezers
inferred← citeshttps://doi.org/10.1021/acs.jafc.5c10020openalex-snapshot
Conformational Dynamics-Driven Engineering of Nanobody Biosensor for Enhanced Detection of Ochratoxin A
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00100openalex-snapshot
Modeling with Alternate Locations in X-ray Protein Structures
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00572openalex-snapshot
Deep Generation Model Guided by the Docking Score for Active Molecular Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00603openalex-snapshot
Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods
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.5b00303openalex-snapshot
CSAR Benchmark of Flexible MedusaDock in Affinity Prediction and Nativelike Binding Pose Selection
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02555openalex-snapshot
Unravelling the Role Played by Non-covalent Interactions in the Action Mechanism of PCDDs within Cells
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00674openalex-snapshot
Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00082openalex-snapshot
Best Practices in Mixed-Solvent Molecular Dynamics and Solvent-Site-Biased Docking
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.7b00188openalex-snapshot
Discovery of Novel and Selective Adenosine A2A Receptor Antagonists for Treating Parkinson’s Disease through Comparative Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00304openalex-snapshot
Exploring the Conformational Landscape of Bioactive Small Molecules
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00754openalex-snapshot
Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b01088openalex-snapshot
Fast Dynamic Docking Guided by Adaptive Electrostatic Bias: The MD-Binding Approach
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b01150openalex-snapshot
Capturing the Flexibility of a Protein–Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques
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.jmedchem.8b01711openalex-snapshot
Determination of Ligand Binding Epitope Structures Using Polarization Transfer from Hyperpolarized Ligands
inferred← citeshttps://doi.org/10.1021/acs.macromol.7b01915openalex-snapshot
Synthesis and Solution-Phase Characterization of Sulfonated Oligothioetheramides
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.4c00502openalex-snapshot
Mining Druggable Sites in Influenza A Hemagglutinin: Binding of the Pinanamine-Based Inhibitor M090
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.8b00523openalex-snapshot
Discovering New Casein Kinase 1d Inhibitors with an Innovative Molecular Dynamics Enabled Virtual Screening Workflow
inferred← citeshttps://doi.org/10.1021/bi201481aopenalex-snapshot
Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein
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/ci100101wopenalex-snapshot
HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations
inferred← citeshttps://doi.org/10.1021/ci100457topenalex-snapshot
Significant Enhancement of Docking Sensitivity Using Implicit Ligand Sampling
inferred← citeshttps://doi.org/10.1021/ci100469nopenalex-snapshot
Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach
inferred← citeshttps://doi.org/10.1021/ci200168bopenalex-snapshot
Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins
inferred← citeshttps://doi.org/10.1021/ci200371zopenalex-snapshot
Approximating Protein Flexibility through Dynamic Pharmacophore Models: Application to Fatty Acid Amide Hydrolase (FAAH)
inferred← citeshttps://doi.org/10.1021/ci2005934openalex-snapshot
Potential and Limitations of Ensemble Docking
inferred← citeshttps://doi.org/10.1021/ci300194aopenalex-snapshot
CRDOCK: An Ultrafast Multipurpose Protein–Ligand Docking Tool
inferred← citeshttps://doi.org/10.1021/ci300244yopenalex-snapshot
Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors
inferred← citeshttps://doi.org/10.1021/ci400025fopenalex-snapshot
CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
inferred← citeshttps://doi.org/10.1021/ci4000294openalex-snapshot
TRAPP: A Tool for Analysis ofTransient BindingPockets inProteins
inferred← citeshttps://doi.org/10.1021/ci400065eopenalex-snapshot
Feasibility of Using Molecular Docking-Based Virtual Screening for Searching Dual Target Kinase Inhibitors
inferred← citeshttps://doi.org/10.1021/ci400087bopenalex-snapshot
The Impact of Molecular Dynamics Sampling on the Performance of Virtual Screening against GPCRs
inferred← citeshttps://doi.org/10.1021/ci400382ropenalex-snapshot
Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures
inferred← citeshttps://doi.org/10.1021/ci500291aopenalex-snapshot
Structure-Based Virtual Screening of the Nociceptin Receptor: Hybrid Docking and Shape-Based Approaches for Improved Hit Identification
inferred← citeshttps://doi.org/10.1021/ci500301sopenalex-snapshot
Ligand–Receptor Affinities Computed by an Adapted Linear Interaction Model for Continuum Electrostatics and by Protein Conformational Averaging
inferred← citeshttps://doi.org/10.1021/ci500414bopenalex-snapshot
Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility
inferred← citeshttps://doi.org/10.1021/ci8003732openalex-snapshot
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes
inferred← citeshttps://doi.org/10.1021/ci9000212openalex-snapshot
Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds
inferred← citeshttps://doi.org/10.1021/ci9003706openalex-snapshot
Molecular Docking Screens Using Comparative Models of Proteins
inferred← citeshttps://doi.org/10.1021/ci9003943openalex-snapshot
Recipes for the Selection of Experimental Protein Conformations for Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci900407copenalex-snapshot
Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
inferred← citeshttps://doi.org/10.1021/ct100246yopenalex-snapshot
Ensemble Docking from Homology Models
inferred← citeshttps://doi.org/10.1021/ct300223copenalex-snapshot
Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design
inferred← citeshttps://doi.org/10.1021/ct500182zopenalex-snapshot
Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design
inferred← citeshttps://doi.org/10.1021/ct5010577openalex-snapshot
The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1021/ct501072topenalex-snapshot
A Collective Variable for the Rapid Exploration of Protein Druggability
inferred← citeshttps://doi.org/10.1021/ja105852yopenalex-snapshot
Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3
inferred← citeshttps://doi.org/10.1021/ja4007468openalex-snapshot
Accounting for Conformational Variability in Protein–Ligand Docking with NMR-Guided Rescoring
inferred← citeshttps://doi.org/10.1021/jm500505fopenalex-snapshot
Targeting Matrix Metalloproteinases: Exploring the Dynamics of the S1′ Pocket in the Design of Selective, Small Molecule Inhibitors
inferred← citeshttps://doi.org/10.1021/jm5010418openalex-snapshot
Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites
inferred← citeshttps://doi.org/10.1021/jp506779yopenalex-snapshot
Assessing the Suitability of the Multilevel Strategy for the Conformational Analysis of Small Ligands
inferred← citeshttps://doi.org/10.1038/s41392-024-02036-3openalex-snapshot
New insights into protein–protein interaction modulators in drug discovery and therapeutic advance
inferred← citeshttps://doi.org/10.1038/s41467-025-59987-6openalex-snapshot
High-speed atomic force microscopy and 3D modeling reveal the structural dynamics of ADAR1 complexes
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