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Application of NMR and Molecular Docking in Structure-Based Drug Discovery
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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Comparing protein–ligand docking programs is difficult
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Comparison of protein active site structures for functional annotation of proteins and drug design
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Critical evaluation of methods to incorporate entropy loss upon binding in high‐throughput docking
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Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
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Binding similarity network of ligand
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Docking and Virtual Screening Using Distributed Grid Technology
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Rational Automatic Search Method for Stable Docking Models of Protein and Ligand
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Knowledge-based scoring function to predict protein-ligand interactions
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FlexE: efficient molecular docking considering protein structure variations
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Crystal structure of human peroxiredoxin 5, a novel type of mammalian peroxiredoxin at 1.5 Å resolution
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Gradient-Tailored Water Suppression for 1H-15N HSQC Experiments Optimized to Retain Full Sensitivity
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A Gradient 13C NOESY-HSQC Experiment for Recording NOESY Spectra of 13C-Labeled Proteins Dissolved in H2O
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Predicting binding modes, binding affinities and ‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function
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Multiple-Start Monte Carlo Docking of Flexible Ligands
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Normal Modes and Essential Dynamics
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Nuclear Magnetic Resonance Metabonomics
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Virtual Screening of Compound Libraries
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The application of high-throughput screening to novel lead discovery
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Application of semiempirical quantum chemical methods as a scoring function in docking
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Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?
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Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
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SOFAST-HMQC Experiments for Recording Two-dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds
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Saturation transfer difference nuclear magnetic resonance study on the specific binding of ligand to protein
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TINS, Target Immobilized NMR Screening: An Efficient and Sensitive Method for Ligand Discovery
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Drug discovery: selecting the optimal approach
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Virtual ligand screening: strategies, perspectives and limitations
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Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches
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Integration of fragment screening and library design
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The application of FAST-NMR for the identification of novel drug discovery targets
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Ligand efficiency and fragment-based drug discovery
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Managing protein flexibility in docking and its applications
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NMR methods in fragment screening: theory and a comparison with other biophysical techniques
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Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR
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NMR methods for the determination of protein–ligand dissociation constants
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Communication Breakdown: Protein Dynamics and Drug Design
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From complete genome sequence to ‘complete’ understanding?
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Sampling of conformation space in torsion angle dynamics calculations
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Nuclear Magnetic Resonance-Based Approaches for Lead Generation in Drug Discovery
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Clustering and similarity of chemical structures represented by binary substructure descriptors
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Solution structure and peptide binding of the SH3 domain from human Fyn
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The SHAPES strategy: an NMR-based approach for lead generation in drug discovery
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Assessing the performance of OMEGA with respect to retrieving bioactive conformations
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Applications of NMR in drug discovery
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Virtual screening and fast automated docking methods
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High-throughput cell-based assays in yeast
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Reliable high-throughput functional screening with 3-FABS
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Reactive compounds and in vitro false positives in HTS
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How many leads from HTS?
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Mean-Force Scoring Functions for Protein–Ligand Binding
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Solution studies of staphylococcal nuclease H124L. 2. Proton, carbon-13, and nitrogen-15 chemical shift assignments for the unligated enzyme and analysis of chemical shift changes that accompany formation of the nuclease-thymidine 3',5'-bisphosphate-calcium ternary complex
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Two-dimensional NMR studies of Staphylococcal nuclease. 1. Sequence-specific assignments of hydrogen-1 signals and solution structure of the nuclease H124L-thymidine 3',5'-bisphosphate-calcium ternary complex
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Two-dimensional NMR studies of staphylococcal nuclease. 2. Sequence-specific assignments of carbon-13 and nitrogen-15 signals from the nuclease H124L-thymidine 3',5'-bisphosphate-calcium ternary complex
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Discovery of Inhibitors of Lupin Diadenosine 5′,5′′′-P1,P4-Tetraphosphate Hydrolase by Virtual Screening
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Estimating Protein−Ligand Binding Affinity Using High-Throughput Screening by NMR
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ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
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A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication
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On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors
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Virtual Exploration of the Chemical Universe up to 11 Atoms of C, N, O, F: Assembly of 26.4 Million Structures (110.9 Million Stereoisomers) and Analysis for New Ring Systems, Stereochemistry, Physicochemical Properties, Compound Classes, and Drug Discovery
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Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
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Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds
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E-Novo: An Automated Workflow for Efficient Structure-Based Lead Optimization
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Steering Protein−Ligand Docking with Quantitative NMR Chemical Shift Perturbations
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Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size
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Protein−Ligand Docking Using Mutually Orthogonal Latin Squares (MOLSDOCK)
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Binding Energy Landscape Analysis Helps to Discriminate True Hits from High-Scoring Decoys in Virtual Screening
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Theory and Applications of NMR-Based Screening in Pharmaceutical Research
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Limits of Free Energy Computation for Protein−Ligand Interactions
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A new analysis of proton chemical shifts in proteins
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HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
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Fluorine-NMR Experiments for High-Throughput Screening: Theoretical Aspects, Practical Considerations, and Range of Applicability
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A General NMR Method for Rapid, Efficient, and Reliable Biochemical Screening
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ALARM NMR: A Rapid and Robust Experimental Method To Detect Reactive False Positives in Biochemical Screens
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FAST-NMR: Functional Annotation Screening Technology Using NMR Spectroscopy
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Rapid Protein−Ligand Costructures Using Chemical Shift Perturbations
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Targeting SDF-1/CXCL12 with a Ligand That Prevents Activation of CXCR4 through Structure-Based Drug Design
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A Common Mechanism Underlying Promiscuous Inhibitors from Virtual and High-Throughput Screening
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Identification and Prediction of Promiscuous Aggregating Inhibitors among Known Drugs
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A Specific Mechanism of Nonspecific Inhibition
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Evaluation of Docking Performance: Comparative Data on Docking Algorithms
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
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Improving Structure-Based Virtual Screening by Multivariate Analysis of Scoring Data
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Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures
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Druggability Indices for Protein Targets Derived from NMR-Based Screening Data
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Receptor Flexibility in de Novo Ligand Design and Docking
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A Critical Assessment of Docking Programs and Scoring Functions
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DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction
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Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
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Contribution of Conformer Focusing to the Uncertainty in Predicting Free Energies for Protein−Ligand Binding
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Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance
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A Critical Assessment of the Performance of Protein−Ligand Scoring Functions Based on NMR Chemical Shift Perturbations
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Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications
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Ligand Binding Efficiency: Trends, Physical Basis, and Implications
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A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
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Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
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Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water*
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Predicting binding modes, binding affinities and `hot spots' for protein-ligand complexes using a knowledge-based scoring function
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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
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Protein ligand docking based on empirical method for binding affinity estimation
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Automated prediction of 15N, 13Cα, 13Cβ and 13C′ chemical shifts in proteins using a density functional database
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Further development and validation of empirical scoring functions for structure-based binding affinity prediction
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Alignment of weakly interacting molecules to protein surfaces using simulations of chemical shift perturbations
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Gene knockdown by large circular antisense for high-throughput functional genomics
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Docking and scoring in virtual screening for drug discovery: methods and applications
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Perspectives on NMR in drug discovery: a technique comes of age
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Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
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Genome-Scale Gene Function Prediction Using Multiple Sources of High-Throughput Data in Yeast Saccharomyces cerevisiae
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Genomes OnLine Database (GOLD): a monitor of genome projects world-wide
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High-throughput protein analysis integrating bioinformatics and experimental assays
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Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery
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Identification of Urinary Biomarkers Useful for Distinguishing a Difference in Mechanism of Toxicity in Rat Model of Cholestasis
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The Sequence of the Human Genome
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Discovering High-Affinity Ligands for Proteins: SAR by NMR
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The Difficult Road from Sequence to Function
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Attenuated T2 relaxation by mutual cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution
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Can sequence determine function?
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Structural and Functional Similarity between the Bacterial Type III Secretion System Needle Protein PrgI and the Eukaryotic Apoptosis Bcl-2 Proteins
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Discovery of fragment molecules that bind the human peroxiredoxin 5 active site. : Screening of human peroxiredoxin 5.
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NMR-based techniques in the hit identification and optimisation processes
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Advances in nuclear magnetic resonance for drug discovery
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Fluorine-NMR Competition Binding Experiments for High-Throughput Screening of Large Compound Mixtures
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Recent Advances in Docking and Scoring
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Fragment-Based Lead Discovery by NMR
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Advances and Challenges in Protein-Ligand Docking
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