How does a drug molecule find its target binding site?

scientific article published on 13 May 2011

How does a drug molecule find its target binding site? is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1021/JA202726Y
P932PMC publication ID3221467
P698PubMed publication ID21545110
P5875ResearchGate publication ID51100721

P50authorMarkus A SeeligerQ56891944
Ron Ofer DrorQ59678272
P2093author name stringDavid E Shaw
Michael P Eastwood
Eric T Kim
Yibing Shan
P2860cites workA conserved protonation-dependent switch controls drug binding in the Abl kinaseQ24657421
Hybrid compound design to overcome the gatekeeper T338M mutation in cSrcQ27655577
Crystal structure of the Src family tyrosine kinase HckQ27734750
Funnels, pathways, and the energy landscape of protein folding: a synthesisQ29617521
Protein kinases: evolution of dynamic regulatory proteinsQ30014836
Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand bindingQ35612259
Blind docking of drug-sized compounds to proteins with up to a thousand residuesQ40352786
Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug designQ41318459
Blind docking of pharmaceutically relevant compounds using RosettaLigandQ42637708
Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular bindingQ73478247
P433issue24
P407language of work or nameEnglishQ1860
P304page(s)9181-9183
P577publication date2011-05-13
P1433published inJournal of the American Chemical SocietyQ898902
P1476titleHow does a drug molecule find its target binding site?
P478volume133

Reverse relations

cites work (P2860)
Q39213631A Hidden Active Site in the Potential Drug Target Mycobacterium tuberculosis dUTPase Is Accessible through Small Amplitude Protein Conformational Changes
Q42381285A Quantitative Model for cAMP Binding to the Binding Domain of MloK1.
Q35156745A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations
Q35687060A drug-specific nanocarrier design for efficient anticancer therapy
Q42380933A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4.
Q34402706ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader
Q36282684Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential
Q33699049Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor
Q57168288Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics
Q36520871Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design
Q47163259Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time
Q41436607Adaptive simulations, towards interactive protein-ligand modeling
Q38800768Advanced molecular dynamics simulation methods for kinase drug discovery
Q38698407Advances in free-energy-based simulations of protein folding and ligand binding.
Q41815533Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis
Q98178435Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning
Q38948740Application of Hidden Markov Models in Biomolecular Simulations.
Q35663714Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Q41969921Atomic and dynamic insights into the beneficial effect of the 1,4-naphthoquinon-2-yl-L-tryptophan inhibitor on Alzheimer's Aβ1-42 dimer in terms of aggregation and toxicity.
Q39264801Atomic level rendering of DNA-drug encounter.
Q55093077Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme.
Q38918905Binding Kinetics in Drug Discovery
Q55476262Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.
Q34254661Binding site multiplicity with fatty acid ligands: implications for the regulation of PKR kinase autophosphorylation with palmitate
Q36009999Bioinformatics and variability in drug response: a protein structural perspective
Q52331594Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics
Q58719254Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview
Q30362300Bringing Clarity to the Prediction of Protein-Ligand Binding Free Energies via "Blurring"
Q35181207Can structural features of kinase receptors provide clues on selectivity and inhibition? A molecular modeling study
Q28484330Can the Energy Gap in the Protein-Ligand Binding Energy Landscape Be Used as a Descriptor in Virtual Ligand Screening?
Q41547898Cloud computing approaches for prediction of ligand binding poses and pathways.
Q37697030Collective variable approaches for single molecule flexible fitting and enhanced sampling
Q38674854Combining experimental and simulation data of molecular processes via augmented Markov models.
Q83987488Comparative Study of Flavins Binding with Human Serum Albumin: A Fluorometric, Thermodynamic, and Molecular Dynamics Approach
Q57975272Computational Approaches for Studying Drug Binding Kinetics
Q33631185Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases
Q26746941Computational approaches in target identification and drug discovery
Q50739068Computational gibberellin‐binding channel discovery unraveling the unexpected perception mechanism of hormone signal by gibberellin receptor
Q26997089Computational methods in drug discovery
Q52620670Conformational dynamics of capping protein and interaction partners: simulation studies
Q30607614Conformational response to ligand binding in phosphomannomutase2: insights into inborn glycosylation disorder.
Q38363774Conformational selection or induced fit? 50 years of debate resolved
Q34440071Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors
Q37377393Construction of Metabolism Prediction Models for CYP450 3A4, 2D6, and 2C9 Based on Microsomal Metabolic Reaction System
Q36553939Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.
Q30667813Critical role of water in the binding of volatile anesthetics to proteins.
Q39757397Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization
Q28546662DnaK as Antibiotic Target: Hot Spot Residues Analysis for Differential Inhibition of the Bacterial Protein in Comparison with the Human HSP70
Q30928104Dominant Alcohol-Protein Interaction via Hydration-Enabled Enthalpy-Driven Binding Mechanism
Q47374327Dynamic Docking: A Paradigm Shift in Computational Drug Discovery
Q34442244Dynamic architecture of a protein kinase.
Q47146818Dynamic changes in binding interaction networks of sex steroids establish their non-classical effects
Q36053324E-pharmacophore-based virtual screening to identify GSK-3β inhibitors
Q27301215Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide
Q38128326Electron transfer in proteins: theory, applications and future perspectives.
Q92882026Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape
Q47110210Energetics of Glutamate Binding to an Ionotropic Glutamate Receptor.
Q88055732Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways
Q37538547Evaluation of a tyrosine kinase peptide microarray for tyrosine kinase inhibitor therapy selection in cancer
Q39257749Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations
Q36582978Explaining why Gleevec is a specific and potent inhibitor of Abl kinase
Q36342813Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4-protein interaction
Q36184063Exploring the Molecular Interactions of 7,8-Dihydroxyflavone and Its Derivatives with TrkB and VEGFR2 Proteins
Q27001129Exploring the role of receptor flexibility in structure-based drug discovery
Q47567885Finding the needle in the haystack: towards solving the protein-folding problem computationally.
Q31033753Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.
Q38574930Flexible receptor docking for drug discovery
Q39338318Fluorescence polarization assay for inhibitors of the kinase domain of receptor interacting protein 1
Q38035239From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine.
Q35655672Functional-segregated coumarin-containing telodendrimer nanocarriers for efficient delivery of SN-38 for colon cancer treatment
Q30539051Funnel metadynamics as accurate binding free-energy method
Q58080237Gaussian accelerated molecular dynamics for elucidation of drug pathways
Q51759998Genome-based approaches to develop epitope-driven subunit vaccines against pathogens of infective endocarditis.
Q34457250High-Throughput parallel blind Virtual Screening using BINDSURF.
Q24614202Highly specific, bisubstrate-competitive Src inhibitors from DNA-templated macrocycles
Q41965081How and when does an anticancer drug leave its binding site?
Q37103848How hydrophobic drying forces impact the kinetics of molecular recognition
Q42377074How wet should be the reaction coordinate for ligand unbinding?
Q30413750Identification of Domains in Protein Structures from the Analysis of Intramolecular Interactions
Q97905427Identification of key interactions between SARS-CoV-2 main protease and inhibitor drug candidates
Q30409188Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics
Q37280290Improved estimation of protein-ligand binding free energy by using the ligand-entropy and mobility of water molecules
Q48044225Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks
Q47671310Insights into the crystal structure of BRD2-BD2 - phenanthridinone complex and theoretical studies on phenanthridinone analogs.
Q93200291Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2
Q58769381Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes
Q39244737Kinetics for Drug Discovery: an industry-driven effort to target drug residence time
Q30655357Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations
Q51604998Let's get honest about sampling.
Q49374902Ligand Binding Pathways and Conformational Transitions of the HIV Protease
Q51083348Ligand entry into the calyx of β-lactoglobulin.
Q57794695Ligand selection from the analysis of protein conformational substates: new leads targeting the N-terminal domain of Hsp90
Q41283780Limiting assumptions in molecular modeling: electrostatics
Q35887173Locating binding poses in protein-ligand systems using reconnaissance metadynamics
Q38970269Lumican Peptides: Rational Design Targeting ALK5/TGFBRI.
Q57489745Mapping the Ligand Binding Landscape
Q26827934Markov state models of biomolecular conformational dynamics
Q33879450Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease.
Q62515266Metal–ligand interactions in drug design
Q47676752Mobility-based prediction of hydration structures of protein surfaces
Q36175542Modeling molecular kinetics with tICA and the kernel trick
Q91588369Molecular Dynamics Simulation for All
Q91452095Molecular Dynamics Simulation reveals the mechanism by which the Influenza Cap-dependent Endonuclease acquires resistance against Baloxavir marboxil
Q27316278Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions
Q30658298Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase
Q41227055Molecular dynamics analysis to evaluate docking pose prediction
Q40844559Molecular dynamics of sialic acid analogues complex with cholera toxin and DFT optimization of ethylene glycol-mediated zinc nanocluster conjugation
Q34061019Molecular dynamics simulations and drug discovery
Q90703205Molecular insights into the interaction of hemorphin and its targets
Q41443980Molecular modeling of methyl-α-Neu5Ac analogues docked against cholera toxin--a molecular dynamics study.
Q43563984Molecular simulation of N-acetylneuraminic acid analogs and molecular dynamics studies of cholera toxin-Neu5Gc complex
Q47952207Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore
Q35822656Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
Q91165293Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins
Q39226865Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases
Q61817296On identifying collective displacements in apo-proteins that reveal eventual binding pathways
Q36654358On the interaction mechanisms of a p53 peptide and nutlin with the MDM2 and MDMX proteins: a Brownian dynamics study.
Q24321210Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization
Q30431383PELE web server: atomistic study of biomolecular systems at your fingertips
Q30503489Pathway and mechanism of drug binding to G-protein-coupled receptors.
Q35578839Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges
Q40458411Peptoid nanosheets exhibit a new secondary-structure motif.
Q36502439Pocket-based drug design: exploring pocket space
Q83615387Potential Selective Inhibitors against Rv0183 of Mycobacterium tuberculosis Targeting Host Lipid Metabolism
Q47625069Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.
Q26749162Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
Q97692526Protein-ligand binding with the coarse-grained Martini model
Q57160189Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach
Q49596794RNA force field with accuracy comparable to state-of-the-art protein force fields
Q39219062Rate Constants and Mechanisms of Protein-Ligand Binding
Q36795631Rational prediction with molecular dynamics for hit identification
Q39152860Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors
Q47291097Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
Q26747130Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations
Q34680443Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase
Q51602802Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution
Q36120365Role of water and steric constraints in the kinetics of cavity-ligand unbinding
Q34300133Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics
Q48247516SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.
Q37680855Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics.
Q50583541Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique
Q60960514Solvents to Fragments to Drugs: MD Applications in Drug Design
Q35819956Specificity quantification of biomolecular recognition and its implication for drug discovery
Q91235937Spontaneous Ligand Access Events to Membrane-Bound Cytochrome P450 2D6 Sampled at Atomic Resolution
Q37277307Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation
Q30423438Structural and dynamic determinants of protein-peptide recognition
Q50470980Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs.
Q28541379Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility
Q35282223Structure-based virtual screening for drug discovery: principles, applications and recent advances.
Q34038269Substrate binding process and mechanistic functioning of type 1 11β-hydroxysteroid dehydrogenase from enhanced sampling methods
Q61811864Surface Binding Energy Landscapes Affect Phosphodiesterase Isoform-Specific Inhibitor Selectivity
Q47250664Systematic exploration of multiple drug binding sites
Q47448946The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions.
Q38061633The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease
Q47292153The bioactive protein-ligand conformation of GluN2C-selective positive allosteric modulators bound to the NMDA receptor.
Q44679907The creation of proton hopping from a drug-receptor encounter
Q34241696The future of molecular dynamics simulations in drug discovery
Q30618624The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.
Q33707352Treating sickle cell disease by targeting HbS polymerization
Q30008744Tyrosine Kinase Activation and Conformational Flexibility: Lessons from Src-Family Tyrosine Kinases.
Q53510547Understanding selective molecular recognition in integrated carbon nanotube-polymer sensors by simulating physical analyte binding on carbon nanotube-polymer scaffolds
Q41996825Unveiling prolyl oligopeptidase ligand migration by comprehensive computational techniques.
Q34787480VinaMPI: facilitating multiple receptor high-throughput virtual docking on high-performance computers.
Q47400859Virtual identification of novel PPARα/γ dual agonists by scaffold hopping of saroglitazar
Q45096401Why is F19Ap53 unable to bind MDM2? Simulations suggest crack propagation modulates binding.

Search more.