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ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Dopamine agonists: structure-activity relationships
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MENTHOR, a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural, biologic, physical, or geometric properties
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A new approach to conformationally restricted peptide analogs: Rigid β-bends. 1. Enkephalin as an example
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A geometric approach to macromolecule-ligand interactions
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Similarity and clustering in chemical information systems
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Pharmacophoric pattern matching in files of 3-D chemical structures: selection of interatomic distance screens
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Identifying 3D maximal common substructures using transputer networks
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Pharmacophoric pattern matching in files of 3D chemical structures: evaluation of search performance
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Pharmacophoric pattern matching in files of 3D chemical structures: comparison of geometric searching algorithms
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Receptor pharmacology and function
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Receptor pharmacology and function
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Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.
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Dopamine D2 receptor binding sites for agonists. A tetrahedral model.
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Amino acids derivatives that stabilize secondary structures of polypeptides--
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Further examples of preferred transition state geometries in the oxidative cyclisation of indole and isoquinoline derivatives
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Chapter 28. Pharmacophore Identification and Receptor Mapping
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Computer-Assisted Drug Design
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The Conformational Parameter in Drug Design: The Active Analog Approach
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Algorithms for the identification of three-dimensional maximal common substructures
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Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
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A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
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Docking flexible ligands to macromolecular receptors by molecular shape
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Drug design by the method of receptor fit
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Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
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Resolution of 5,6-Dihydroxy-2-(N,N-di -n-propylamino)tetralin in Relation to the Structural and Stereochemical Requirements for Centrally Acting Dopamine Agonists
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Three-Dimensional Molecular Modeling and Drug Design
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Real-Time Color Graphics in Studies of Molecular Interactions

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Conformational Flexibility in 3 D Structure Searching
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High‐throughput ‘Virtual’ Chemistry
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Structure and Substructure Searching
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Three‐dimensional Structure Searching
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Enzyme Inhibitors
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Molecular Modeling in Drug Design
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Virtual Screening
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Virtual Screening
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Docking, Scoring, and Virtual Screening in Drug Discovery
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Calculation of Structure Descriptors
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A Perspective of Modern Methods in Computer‐Aided Drugc design
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Recent Advances in Ligand Design Methods
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Theoretical and Practical Aspects of Three‐Dimensional Quantitative Structure‐Activity Relationships
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Searching Techniques for Databases of Three‐Dimensional Chemical Structures
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New Computational Approaches to Predict Protein‐Ligand Interactions
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Pharmacophore Pattern Application in Virtual Screening. Library Design and QSAR
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Small Molecules
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Pharmacophore Modeling: 1 – Methods
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Virtual Screening
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Pharmacophore Modeling: 1 – Methods
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Drug design: the present and the future
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Chapter 29. Macromolecular X-Ray Crystallography and NMR as Tools for Structure-based Drug Design
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Chapter 29. 3D Database Searching and Docking Strategles
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Identifying small-molecule lead compounds: The screening approach to drug discovery
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Chapter 11 Site-Directed Computer-Aided Drug Design: Progress Towards the Design of Novel Lead Compounds Using ‘Molecular’ Lattices
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Structure-based drug design
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Cyclic HIV protease inhibitors capable of displacing the active site structural water molecule
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Virtual screening—an overview
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Pharmacophore methods
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Interactive and Versatile Navigation of Structural Databases
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Diverse Viewpoints on Computational Aspects of Molecular Diversity
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A Web-Based 3D-Database Pharmacophore Searching Tool for Drug Discovery
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De Novo Generation of Molecular Structures Using Optimization To Select Graphs on a Given Lattice
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From Structure Diagrams to Visual Chemical Patterns
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Fighting High Molecular Weight in Bioactive Molecules with Sub-Pharmacophore-Based Virtual Screening
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Setting the Record Straight: The Origin of the Pharmacophore Concept
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Flexophore, a New Versatile 3D Pharmacophore Descriptor That Considers Molecular Flexibility
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Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size
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RASSE: A New Method for Structure-Based Drug Design
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“Shrink-Wrap” Surfaces: A New Method for Incorporating Shape into Pharmacophoric 3D Database Searching
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3DFS: A New 3D Flexible Searching System for Use in Drug Design
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Superposition of Three-Dimensional Chemical Structures Allowing for Conformational Flexibility by a Hybrid Method
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Fast Similarity Search in Three-Dimensional Structure Databases
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TreeDock: A Tool for Protein Docking Based on Minimizing van der Waals Energies
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One-Dimensional Molecular Representations and Similarity Calculations: Methodology and Validation
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Pruned Receptor Surface Models and Pharmacophores for Three-Dimensional Database Searching
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Searching Techniques for Databases of Two- and Three-Dimensional Chemical Structures
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Strategies for the determination of pharmacophoric 3D database queries
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A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching
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Mass Receptor Screening for New Drugs
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Strategies for Indirect Computer-Aided Drug Design
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QSAR Analysis of the Inhibition of Recombinant CYP 3A4 Activity by Structurally Diverse Compounds Using a Genetic Algorithm-Combined Partial Least Squares Method
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Receptor-based prediction of binding affinities
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The Practice of Structure Activity Relationships (SAR) in Toxicology
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Rule-Based Deconstruction and Reconstruction of Diterpene Libraries: Categorizing Patterns & Unravelling the Structural Landscape
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De novo design of ligands /spl lsqb/automated drug design/spl rsqb/
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AutoGrow: A Novel Algorithm for Protein Inhibitor Design
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Structure-Based Strategies for Drug Design and Discovery
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Rational Design of Potent, Bioavailable, Nonpeptide Cyclic Ureas as HIV Protease Inhibitors
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Efficient algorithms for generalized subgraph query processing
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The Discovery of Novel Selective D1 Dopaminergic Agonists: A-68930, A-77636, A-86929, and ABT-413
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Pharmacophore Discovery: A Critical Review
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Pharmacophore Discovery
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Use of 3D Pharmacophore Models in 3D Database Searching
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Toward Commercialization
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Development of a Three-Dimensional Substructure Search Program for Organic Molecules
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Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design
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Computer Aided Drug Design: Success and Limitations
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History and Evolution of the Pharmacophore Concept in Computer-Aided Drug Design
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Die post-SELEX Optimierung des Trypanosomen-spezifischen RNA-Aptamers 2-16
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Comparative Modeling of Proteins in the Design of Novel Renin Inhibitors
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Efficient techniques for subgraph mining and query processing
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A Data Resource for Sulfuric Acid Reactivity of Organic Chemicals
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Molecular Docking and Structure-Based Drug Design Strategies
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Virtual Screening: A Fast Tool for Drug Design
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