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The Role of Virtual Screening in Computer Aided Structure-Based Drug Design
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Critical evaluation of search algorithms for automated molecular docking and database screening
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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BLEEP?potential of mean force describing protein-ligand interactions: I. Generating potential
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Hydrophilicity of cavities in proteins
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The particle concept: placing discrete water molecules during protein-ligand docking predictions
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Small Molecule Docking and Scoring
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Structural stability of binding sites: Consequences for binding affinity and allosteric effects
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Application and Limitations of X‐ray Crystallographic Data in Structure‐Based Ligand and Drug Design
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Three‐dimensional structure of the complex of 4‐guanidino‐Neu5Ac2en and influenza virus neuraminidase
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Virtual screening to enrich hit lists from high‐throughput screening: A case study on small‐molecule inhibitors of angiogenin
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ICM‐DISCO docking by global energy optimization with fully flexible side‐chains
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Patterns for Prediction of Hydration around Polar Residues in Proteins
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Contribution of Buried Hydrogen Bonds to Protein Stability The Crystal Structures of Two Barnase Mutants
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The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria
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X-SITE: Use of Empirically Derived Atomic Packing Preferences to Identify Favourable Interaction Regions in the Binding Sites of Proteins
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Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm
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Knowledge-based scoring function to predict protein-ligand interactions
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Docking ligands onto binding site representations derived from proteins built by homology modelling
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FlexE: efficient molecular docking considering protein structure variations
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Binding site characteristics in structure-based virtual screening: evaluation of current docking tools
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WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes
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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
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High-throughput docking as a source of novel drug leads
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Predictive ADMET studies, the challenges and the opportunities
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Testing a Flexible-receptor Docking Algorithm in a Model Binding Site
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Contribution of Translational and Rotational Motions to Molecular Association in Aqueous Solution
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Assessment of the role of the fibronectin-like domain of gelatinase A by analysis of a deletion mutant.
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NMR Studies of the Backbone Flexibility and Structure of Human Growth Hormone: A Comparison of High and Low pH Conformations
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A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology
inferredcites →https://doi.org/10.1016/s0022-2836(05)80038-5openalex-snapshot
Ligand docking to proteins with discrete side-chain flexibility
inferredcites →https://doi.org/10.1016/s0026-895x(24)23192-8openalex-snapshot
Accommodating Protein Flexibility in Computational Drug Design,
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Ligand-selective receptor conformations revisited: the promise and the problem
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The price of innovation: new estimates of drug development costs
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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1
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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
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The basis of the hydrophobic effect
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Drug-like properties and the causes of poor solubility and poor permeability
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A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening
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LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
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Miniaturization technologies in HTS: how fast, how small, how soon?
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High-throughput docking for lead generation
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Evolution and Physics in Comparative Protein Structure Modeling
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Is There a Difference between Leads and Drugs? A Historical Perspective
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Algorithm for the systematic solvation of proteins based on the directionality of hydrogen bonds
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Host-guest supramolecular chemistry. 34. The incremental approach to noncovalent interactions: coulomb and van der Waals effects in organic ion pairs
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The cost of conformational order: entropy changes in molecular associations
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SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence
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Inclusion of Loss of Translational and Rotational Freedom in Theoretical Estimates of Free Energies of Binding. Application to a Complex of Benzene and Mutant T4 Lysozyme
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Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model
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Structure-Based Approach for the Discovery of Bis-benzamidines as Novel Inhibitors of Matriptase
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Detailed Analysis of Scoring Functions for Virtual Screening
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Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data
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Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds
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Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
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A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
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Structure-Based Generation of a New Class of Potent Cdk4 Inhibitors: New de Novo Design Strategy and Library Design
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Structural Studies of the Resistance of Influenza Virus Neuramindase to Inhibitors
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Molecular Docking and High-Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase-1B
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Simple Selection Criteria for Drug-like Chemical Matter
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Docking into Knowledge-Based Potential Fields: A Comparative Evaluation of DrugScore
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Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes
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Performance of 3D-Database Molecular Docking Studies into Homology Models
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Discovery of Potent Inhibitors of Dihydroneopterin Aldolase Using CrystaLEAD High-Throughput X-ray Crystallographic Screening and Structure-Directed Lead Optimization
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Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding
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Discovery of a Potent and Selective Protein Kinase CK2 Inhibitor by High-Throughput Docking
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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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Pairwise GB/SA Scoring Function for Structure-based Drug Design
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Multiple automatic base selection: Protein–ligand docking based on incremental construction without manual intervention
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Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase
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Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
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Fast prediction and visualization of protein binding pockets with PASS
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Virtual screening with solvation and ligand-induced complementarity
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A validation study on the practical use of automated de novo design
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Comparative study of several algorithms for flexible ligand docking
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Discovering novel ligands for macromolecules using X-ray crystallographic screening
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Structural genomics in the biotechnology sector.
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Structure-aided drug design's next generation
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ADMET in silico modelling: towards prediction paradise?
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Key factors in the rising cost of new drug discovery and development
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High-throughput crystallography for lead discovery in drug design
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Integration of virtual and high-throughput screening
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High-resolution crystallographic studies of native concanavalin A using rapid Laue data collection methods and the introduction of a monochromatic large-angle oscillation technique (LOT)
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Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking
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Enthalpy of hydrogen bond formation in aprotein-ligand binding reaction.
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Structure-based design of an osteoclast-selective, nonpeptide Src homology 2 inhibitor with in vivo antiresorptive activity
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Structural genomics: Computational methods for structure analysis
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Multiple diverse ligands binding at a single protein site: A matter of pre‐existing populations
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A Single Glycine Residue at the Entrance to the First Membrane-Spanning Domain of the γ-Aminobutyric Acid Type A Receptor β2Subunit Affects Allosteric Sensitivity to GABA and Anesthetics
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Discovering High-Affinity Ligands for Proteins: SAR by NMR
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Discovering High-Affinity Ligands for Proteins
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Drug Discovery: A Historical Perspective
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Molecular Recognition and Docking Algorithms
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High Throughput Screening for Drug Discovery: Continually Transitioning into New Technology
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In silico discovery of novel Retinoic Acid Receptor agonist structures
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Combinatorial chemistry. Facing the challenge of chemical genomics
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Predicting Molecular Interactions in silico: II. Protein-Protein and Protein- Drug Docking
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Virtual Screening in Lead Discovery: A Viewpoint
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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A De Novo Designed Inhibitor of D ‐Ala– D ‐Ala Ligase from E. coli
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A De Novo Designed Inhibitor of D ‐Ala– D ‐Ala Ligase from E. coli
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The Role of Virtual Screening in Computer Aided Structure‐Based Drug Design
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Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening
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A Novel Search Engine for Virtual Screening of Very Large Databases
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Hydration Properties of Ligands and Drugs in Protein Binding Sites: Tightly-Bound, Bridging Water Molecules and Their Effects and Consequences on Molecular Design Strategies
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In Silico Drug Screening Approach for the Design of Magic Bullets: A Successful Example with Anti-HIV Fullerene Derivatized Amino Acids
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The First de Novo-Designed Antagonists of the Human NK2 Receptor
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Analysis of Enoyl‐Acyl Carrier Protein Reductase Structure and Interactions Yields an Efficient Virtual Screening Approach and Suggests a Potential Allosteric Site
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Shape-based Machine Learning Models for the Potential Novel COVID-19 Protease Inhibitors Assisted by Molecular Dynamics Simulation
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