Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

scientific article (publication date: 2 August 2002)

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O
P3181OpenCitations bibliographic resource ID3863370
P698PubMed publication ID12203463

P50authorGerhard KlebeQ24262166
P2093author name stringHolger Gohlke
P433issue15
P407language of work or nameEnglishQ1860
P921main subjectmacromoleculeQ178593
P304page(s)2644-76
P577publication date2002-08-02
P13046publication type of scholarly workreview articleQ7318358
P1433published inAngewandte ChemieQ538683
P1476titleApproaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
P478volume41

Reverse relations

cites work (P2860)
Q46639902(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding
Q87378606A Matter of Order: How E‐Selectin Makes Sweet Contacts
Q34721619A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes
Q42418169A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations.
Q51543578A novel, customizable and optimizable parameter method using spherical harmonics for molecular shape similarity comparisons
Q45199575A spectroscopic and photophysical study on molecular recognition via hydrogen-bonding and pi-pi stacking interactions
Q36239113A unifying review of bioassay-guided fractionation, effect-directed analysis and related techniques.
Q30386091Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions
Q37920386Advances and applications of binding affinity prediction methods in drug discovery
Q47280371Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors
Q42238419Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors
Q37409322An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics
Q90010732An account of solvent accessibility in protein-RNA recognition
Q33408373An effective docking strategy for virtual screening based on multi-objective optimization algorithm
Q46378945An improved method to predict the entropy term with the MM/PBSA approach.
Q36838120An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
Q37683442Analysis of cooperativity by isothermal titration calorimetry
Q44203281Antigen–Antibody Interactions and Structural Flexibility of a Femtomolar-Affinity Antibody
Q93016939Antimalarial Properties of Isoquinoline Derivative from Streptomyces hygroscopicus subsp. Hygroscopicus: An In Silico Approach
Q50111842Application of computational methods for anticancer drug discovery, design, and optimization
Q30370841Application of the 4D fingerprint method with a robust scoring function for scaffold-hopping and drug repurposing strategies.
Q89217077Application of the quantum mechanical IEF/PCM-MST hydrophobic descriptors to selectivity in ligand binding
Q85323845Are Homology Models Sufficiently Good for Free-Energy Simulations?
Q30835329Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set.
Q55037679Assessing the stability of free-energy perturbation calculations by performing variations in the method
Q62582760Assessment of Docking Poses:  Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations
Q29619637Benchmarking sets for molecular docking
Q30392142Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties
Q35568225Binding Affinities of Host–Guest, Protein–Ligand, and Protein–Transition‐State Complexes
Q56975687Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods
Q48023567Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.
Q33202843Binding affinity prediction with different force fields: examination of the linear interaction energy method
Q33757755Binding affinity prediction with property-encoded shape distribution signatures
Q37588656Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).
Q58860073Binding free energy calculations and biological testing of novel thiobarbiturates as inhibitors of the human NAD+dependent histone deacetylase Sirt2
Q37372747Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".
Q38344912Binding selectivity of RecA to a single stranded DNA, a computational approach
Q37363075Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations
Q34061956Biology-oriented synthesis
Q36191972Biophysical Limits of Protein–Ligand Binding
Q30044592Building a virtual ligand screening pipeline using free software: a survey
Q35263970CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.
Q45710657Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field
Q51914537Calculations of protein-ligand binding entropy of relative and overall molecular motions
Q47361378Can MM/GBSA calculations be sped up by system truncation?
Q59294029Classifying Calpain Inhibitors for the Treatment of Cataracts: A Self Organising Map (SOM) ANN/KM Approach in Drug Discovery
Q49539854Computational and Pharmacological Evaluation of Ferrocene-Based Acyl Ureas and Homoleptic Cadmium Carboxylate Derivatives for Anti-diabetic Potential.
Q30398071Computational methods in drug discovery.
Q37335295Computations of standard binding free energies with molecular dynamics simulations
Q38916780Computer-aided discovery of anti-HIV agents
Q61813251Conserved Disease Modules Extracted From Multilayer Heterogeneous Disease and Gene Networks for Understanding Disease Mechanisms and Predicting Disease Treatments
Q34145063Constraining binding hot spots: NMR and molecular dynamics simulations provide a structural explanation for enthalpy-entropy compensation in SH2-ligand binding
Q37357274Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.
Q39900683Cooperative heparin-mediated oligomerization of fibroblast growth factor-1 (FGF1) precedes recruitment of FGFR2 to ternary complexes.
Q38112830Correlating Structure and Energetics in Protein-Ligand Interactions: Paradigms and Paradoxes
Q84465569Correlation between biological activity and binding energy in systems of integrin with cyclic RGD-containing binders: a QM/MM molecular dynamics study
Q85200609Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di‐mannose deoxy analogs with P51G‐m4‐Cyanovirin‐N
Q27641371D-Phe-Pro-Arg type thrombin inhibitors: unexpected selectivity by modification of the P1 moiety
Q39726767DEKOIS: Demanding Evaluation Kits for Objective in Silico Screening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions
Q50493869Deciphering the mechanisms of selective inhibition for the tandem BD1/BD2 in the BET-bromodomain family
Q30350781Decoys for docking
Q56979637Designing a ligand for pharmaceutical purposes
Q37581863Development of extracellular signal-regulated kinase inhibitors.
Q42251037Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking
Q36280727Discovery of Novel ROCK1 Inhibitors via Integrated Virtual Screening Strategy and Bioassays
Q34364227Docking and scoring in virtual screening for drug discovery: methods and applications
Q33527932Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function
Q34563828Docking-Based Virtual Screening of Covalently Binding Ligands: An Orthogonal Lead Discovery Approach
Q28732341Drug design for ever, from hype to hope
Q34536280Drug repositioning by structure-based virtual screening
Q34571023Drugs, their targets and the nature and number of drug targets
Q41459981Dynamics of Hydration Water Plays a Key Role in Determining the Binding Thermodynamics of Protein Complexes
Q41481809EMBM − A New Enzyme Mechanism-Based Method for Rational Design of Chemical Sites of Covalent Inhibitors
Q30362956Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.
Q37307959Efficient drug lead discovery and optimization
Q34908421Emerging methods for ensemble-based virtual screening
Q38792709Empirical Scoring Functions for Affinity Prediction of Protein-ligand Complexes
Q57492456Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges
Q37439036Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization
Q39505064Enhanced accumulation of low-molecular-weight chitosan in kidneys: a study on the influence of N-acetylation of chitosan on the renal targeting.
Q80988436Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields
Q91163608Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations
Q41815648Evaluation of different virtual screening programs for docking in a charged binding pocket
Q30358437Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge.
Q83133195Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction
Q56989244Exploring the free-energy landscape of carbohydrate–protein complexes: development and validation of scoring functions considering the binding-site topology
Q35089889FADB: a food additive molecular database for in silico screening in food toxicology
Q27998699Fast automated placement of polar hydrogen atoms in protein-ligand complexes
Q39645443Free Energy Calculations on Snake Venom Metalloproteinase BaP1
Q87611444Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies
Q34153589From laptop to benchtop to bedside: structure-based drug design on protein targets.
Q35070393Functional characterization of ECP-heparin interaction: a novel molecular model
Q42314941General van der Waals potential for common organic molecules
Q47250694HawkRank: a new scoring function for protein-protein docking based on weighted energy terms.
Q34338992Higher throughput calorimetry: opportunities, approaches and challenges
Q51309493How Good Are State-of-the-Art Docking Tools in Predicting Ligand Binding Modes in Protein–Protein Interfaces?
Q47793987How accurate are continuum solvation models for drug-like molecules?
Q47299688How accurate is the description of ligand-protein interactions by a hybrid QM/MM approach?
Q43630348How far can virtual screening take us in drug discovery?
Q51860628How sophisticated should a scoring function be to ensure successful docking, scoring and virtual screening?
Q57296153Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation
Q27701726Identification of a β1/β2-specific sulfonamide proteasome ligand by crystallographic screening
Q48321338Identification of potential aryl hydrocarbon receptor ligands by virtual screening of industrial chemicals.
Q36320975Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target
Q85306744Impact of protein binding cavity volume (PCV) and ligand volume (LV) in rigid and flexible docking of protein–ligand complexes
Q40130726In Silico Characterization of the Binding Affinity of Dendrimers to Penicillin-Binding Proteins (PBPs): Can PBPs be Potential Targets for Antibacterial Dendrimers?
Q44970440In Silico-Screening Approaches for Lead Generation: Identification of Novel Allosteric Modulators of Human-Erythrocyte Pyruvate Kinase
Q36840592In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling
Q28540772Inhibition of catalase by tea catechins in free and cellular state: a biophysical approach
Q47763550Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches
Q53771347Insight into drug resistance mechanisms and discovery of potential inhibitors against wild-type and L1196M mutant ALK from FDA-approved drugs
Q80095175Integrated approach using protein and ligand information to analyze selectivity- and affinity-determining features of carbonic anhydrase isozymes
Q39211734Interaction of polyhexamethylene biguanide hydrochloride (PHMB) with phosphatidylcholine containing o/w emulsion and consequences for microbicidal efficacy and cytotoxicity
Q45022698Interactions of 5-deazapteridine derivatives with Mycobacterium tuberculosis and with human dihydrofolate reductases
Q34018803Label-free microfluidic characterization of temperature-dependent biomolecular interactions
Q36579823Ligand binding mode prediction by docking: mdm2/mdmx inhibitors as a case study
Q34754684Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations.
Q34614404Ligand-Induced Protein Mobility in Complexes of Carbonic Anhydrase II and Benzenesulfonamides with Oligoglycine Chains
Q82599858MM/GBSA and LIE estimates of host–guest affinities: dependence on charges and solvation model
Q27689469Methyl, ethyl, propyl, butyl: futile but not for water, as the correlation of structure and thermodynamic signature shows in a congeneric series of thermolysin inhibitors
Q37055383Microfluidics for drug discovery and development: from target selection to product lifecycle management
Q39289157Microscopic Modes and Free Energies for Topoisomerase I-DNA Covalent Complex Binding with Non-campothecin Inhibitors by Molecular Docking and Dynamics Simulations
Q41682682Modeling, molecular docking, probing catalytic binding mode of acetyl-CoA malate synthase G in Brucella melitensis 16M.
Q35150471Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
Q35912029Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies
Q40854828Molecular Modeling of Geometries, Charge Distributions, and Binding Energies of Small, Druglike Molecules Containing Nitrogen Heterocycles and Exocyclic Amino Groups in the Gas Phase and in Aqueous Solution
Q33472678Molecular determinants of juvenile hormone action as revealed by 3D QSAR analysis in Drosophila
Q40374329Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors.
Q35829041Molecular evolution of affinity and flexibility in the immune system
Q54577952Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM–GBSA calculation
Q39676629Molecular simulation methods in drug discovery: a prospective outlook
Q43244976Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12.
Q42659257One Size Does Not Fit All: The Limits of Structure-Based Models in Drug Discovery
Q52633245Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor.
Q42182002PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements
Q33893098Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.
Q30582334Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes
Q34373691Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion
Q51372865Predicting the impact of mutations on the specific activity of Bacillus thermocatenulatus lipase using a combined approach of docking and molecular dynamics
Q34249481Prediction of SAMPL3 host–guest binding affinities: evaluating the accuracy of generalized force-fields
Q27703161Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method
Q30495095Prediction of the water content in protein binding sites
Q83072123Prediction of zanamivir efficiency over the possible 2009 influenza A (H1N1) mutants by multiple molecular dynamics simulations and free energy calculations
Q33209836ProPose: a docking engine based on a fully configurable protein-ligand interaction model
Q35750168Probing the Effect of Conformational Constraint on Phosphorylated Ligand Binding to an SH2 Domain Using Polarizable Force Field Simulations
Q46048965Probing the interaction of lysozyme with ciprofloxacin in the presence of different-sized Ag nano-particles by multispectroscopic techniques and isothermal titration calorimetry
Q90153399Proposing the Promiscuous Protein Structures in JNK1 and JNK3 for Virtual Screening in Pursuit of Potential Leads
Q37384155Protein-Ligand Interactions: Thermodynamic Effects Associated with Increasing the Length of an Alkyl Chain
Q51398366Protein–Ligand Binding Free Energies from Exhaustive Docking
Q27675114Protein–Ligand Interactions: Thermodynamic Effects Associated with Increasing Nonpolar Surface Area
Q27683926Protein–ligand interactions: Probing the energetics of a putative cation–π interaction
Q38124417Protonation and pK changes in protein-ligand binding.
Q37934799Putting anion-π interactions into perspective
Q86001715Quantification of the Effect of Conformational Restriction on Supramolecular Effective Molarities
Q34063684Quantification of the effects of ionic strength, viscosity, and hydrophobicity on protein-ligand binding affinity
Q44234859Quantitative insights towards the design of potent deazaxanthine antagonists of adenosine 2B receptors
Q30381275Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction.
Q55016340Quantum Chemical Approaches in Structure-Based Virtual Screening and Lead Optimization.
Q39675574Rapid activity prediction of HIV-1 integrase inhibitors: harnessing docking energetic components for empirical scoring by chemometric and artificial neural network approaches
Q82039592Rapid probe and isolation of bioactive compounds from Dioscorea panthaica using human serum albumin functionalized magnetic nano-particles (HSA-MNPs)-based ligand fishing coupled with electrospray ionization mass spectrometry
Q97074440Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations
Q39067502Refinement, Reduction, and Replacement of Animal Toxicity Tests by Computational Methods
Q44109422Regulatory mechanism of the light-activable allosteric switch LOV-TAP for the control of DNA binding: a computer simulation study.
Q33893521Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method
Q48050957Relative Binding Free Energy Calculations Applied to Protein Homology Models
Q30399241Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations
Q35156305Resolving hot spots in the C-terminal dimerization domain that determine the stability of the molecular chaperone Hsp90
Q34867886SimG: An Alignment Based Method for Evaluating the Similarity of Small Molecules and Binding Sites
Q79363830Smart drug discovery leveraging innovative technologies and predictive knowledge
Q56890026Solvated Interaction Energy (SIE) for Scoring Protein–Ligand Binding Affinities. 2. Benchmark in the CSAR-2010 Scoring Exercise
Q27677099Specificity of Processing  -Glucosidase I Is Guided by the Substrate Conformation: CRYSTALLOGRAPHIC AND IN SILICO STUDIES
Q35635713Statistical potential for modeling and ranking of protein-ligand interactions
Q41785296Strategic Targeting of Multiple Water‐Mediated Interactions: A Concise and Rational Structure‐Based Design Approach to Potent and Selective MMP‐13 Inhibitors
Q42988079Structural Modeling of HCV NS3/4A Serine Protease Drug-Resistance Mutations Using End-Point Continuum Solvation and Side-Chain Flexibility Calculations
Q35080520Structural basis for the high-affinity inhibition of mammalian membranous adenylyl cyclase by 2',3'-o-(N-methylanthraniloyl)-inosine 5'-triphosphate.
Q51661462Structure‐based quantitative structure‐activity relationship studies of checkpoint kinase 1 inhibitors
Q47316545Symmetrical Parameterization of Rigid Body Transformations for Biomolecular Structures
Q41416858Synthesis, Biological Evaluation and Molecular Modeling of Substituted Indeno[1,2-b]indoles as Inhibitors of Human Protein Kinase CK2.
Q39512241Target Flexibility in RNA-Ligand Docking Modeled by Elastic Potential Grids
Q48570844Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers
Q63360901The -glycan structures of the antigenic variants of chlorovirus PBCV-1 major capsid protein help to identify the virus-encoded glycosyltransferases
Q27012984The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
Q52857114The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein-ligand interactions and implicit COSMO solvation
Q57128379The Solvated Interaction Energy Method for Scoring Binding Affinities
Q57901310The importance of solvation in the design of ligands targeting membrane proteins
Q51599141The quest for novel chemical matter and the contribution of computer-aidedde novodesign
Q57096110Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase
Q27702163Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data
Q51039120Toward quantitative estimates of binding affinities for protein-ligand systems involving large inhibitor compounds: a steered molecular dynamics simulation route
Q57009165Towards an Integrated Description of Hydrogen Bonding and Dehydration: Decreasing False Positives in Virtual Screening with the HYDE Scoring Function
Q37014096Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.
Q37696666Troubleshooting computational methods in drug discovery
Q37364377Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential
Q33642484Trypsin-ligand binding free energy calculation with AMOEBA.
Q86314270Two Distinct Thermal Stabilities of DNA and Enzymatic Activities of DNase I in a Multistep Assembly with Carbazole Ligands: Different Binding Characteristics for Duplex and Quadruplex DNA
Q58768392Unraveling the mechanism of the cadherin-catenin-actin catch bond
Q46306239Virtual Screening Approach of Bacterial Peptide Deformylase Inhibitors Results in New Antibiotics.
Q33247681Virtual ligand screening: strategies, perspectives and limitations
Q30366496Virtual screening: an in silico tool for interlacing the chemical universe with the proteome.
Q42059670Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT.
Q38059796What in silico molecular docking can do for the 'bench-working biologists'.
Q27656255ZINC--a free database of commercially available compounds for virtual screening
Q44505963ZZ made EZ: influence of inhibitor configuration on enzyme selectivity.
Q47166149eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations.

Search more.