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Active-site-directed 3D database searching: Pharmacophore extraction and validation of hits

https://doi.org/10.1007/bf00124472
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What this work says

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

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Three‐Dimensional Structure Database Searches
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Searching Techniques for Databases of Three‐Dimensional Chemical Structures
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ChemInform Abstract: Searching Techniques for Databases of Three‐Dimensional Chemical Structures.
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Automated docking with grid‐based energy evaluation
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Protein targets for structure‐based drug design
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CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure
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Orientational sampling and rigid‐body minimization in molecular docking
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The Use of Composite Crystal-field Environments in Molecular Recognition and the de Novo Design of Protein Ligands
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Three-Dimensional Pharmacophoric Pattern Searching
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PRO_LIGAND: An approach to de novo molecular design. 1. Application to the design of organic molecules
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FLOG: A system to select ?quasi-flexible? ligands complementary to a receptor of known three-dimensional structure
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On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure
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PRO_LIGAND: An approach to de novo molecular design. 6. Flexible fitting in the design of peptides
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Sampling conformational hyperspace: Techniques for improving completeness
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A genetic algorithm for flexible molecular overlay and pharmacophore elucidation
inferredcites →https://doi.org/10.1007/bf00124360openalex-snapshot
A Monte Carlo pharmacophore generation procedure: Application to the human PAF receptor
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The computer program LUDI: A new method for the de novo design of enzyme inhibitors
inferredcites →https://doi.org/10.1007/bf00124408openalex-snapshot
A genetic algorithm for the automated generation of molecules within constraints
inferredcites →https://doi.org/10.1007/bf00124460openalex-snapshot
Functionality map analysis of the active site cleft of human thrombin
inferredcites →https://doi.org/10.1007/bf00125665openalex-snapshot
Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances
inferredcites →https://doi.org/10.1007/bf00126217openalex-snapshot
LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
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Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities
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A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists
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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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Constrained search of conformational hyperspace
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A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies
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Reviews in Computational Chemistry, Vol. 8
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A geometric approach to macromolecule-ligand interactions
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Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges
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How accurate does a force field need to be?
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Pharmacophoric pattern matching in files of 3-D chemical structures: selection of interatomic distance screens
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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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Pharmacophoric pattern matching in files of three-dimensional chemical structures: use of bounded distance matrices for the representation and searching of conformationally flexible molecules
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AN EFFICIENT BOUNDING SPHERE
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In vitro and in vivo characterization of a neutral boron-containing thrombin inhibitor.
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Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors.
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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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Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited
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Estimation of aqueous solubility of organic molecules by the group contribution approach. Application to the study of biodegradation
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CONCORD and CAMBRIDGE: comparison of computer generated chemical structures with x-ray crystallographic data
inferredcites →https://doi.org/10.1021/ci00014a019openalex-snapshot
Chem-X and CAMBRIDGE. Comparison of computer generated chemical structures with x-ray crystallographic data
inferredcites →https://doi.org/10.1021/ci00016a013openalex-snapshot
Comparison of conformations of small molecule structures from the Protein Data Bank with those generated by Concord, Cobra, ChemDBS-3D, and Converter and those extracted from the Cambridge Structural Database
inferredcites →https://doi.org/10.1021/ci00017a024openalex-snapshot
Conformational searching in ISIS/3D databases
inferredcites →https://doi.org/10.1021/ci00017a025openalex-snapshot
Flexible 3D searching: The directed tweak technique
inferredcites →https://doi.org/10.1021/ci00017a026openalex-snapshot
Pharmacophoric pattern matching in files of three-dimensional chemical structures: Comparison of conformational-searching algorithms for flexible searching
inferredcites →https://doi.org/10.1021/ci00020a039openalex-snapshot
Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures
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SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
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Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics
inferredcites →https://doi.org/10.1021/ci00064a005openalex-snapshot
3DSEARCH: a system for three-dimensional substructure searching
inferredcites →https://doi.org/10.1021/ci00067a016openalex-snapshot
Conformational freedom in 3-D databases. 1. Techniques
inferredcites →https://doi.org/10.1021/ci9500851openalex-snapshot
Similarity Searching in Files of Three-Dimensional Chemical Structures. Alignment of Molecular Electrostatic Potential Fields with a Genetic Algorithm
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MOLMAKER: De Novo Generation of 3D Databases for Use in Drug Design
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Identification of Common Functional Configurations Among Molecules
inferredcites →https://doi.org/10.1021/ci960002wopenalex-snapshot
Similarity Searching in Files of Three-Dimensional Chemical Structures: Flexible Field-Based Searching of Molecular Electrostatic Potentials
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From atoms and bonds to three-dimensional atomic coordinates: automatic model builders
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Determination of Pharmacophoric Geometry for Collagenase Inhibitors Using a Novel Computational Method and Its Verification Using Molecular Dynamics, NMR, and X-ray Crystallography
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Rationally Designed N,N'-Bis[(N-p-guanidinobenzyl-N-methyl)aminocarbonyl]-1,3-diaminobenzene , "BIGBEN", Binds to the Minor Groove of d(CGCGAATTCGCG)2 as Determined by Two-Dimensional Nuclear Magnetic Resonance Spectroscopy
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Receptor Surface Models. 1. Definition and Construction
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Novel Angiotensin II Receptor Antagonists. Design, Synthesis, and in Vitro Evaluation of Dibenzo[a,d]cycloheptene and Dibenzo[b,f]oxepin Derivatives. Searching for Bioisosteres of Biphenyltetrazole Using a Three-Dimensional Search Technique
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Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes
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The Discovery of Novel, Structurally Diverse Protein Kinase C Agonists through Computer 3D-Database Pharmacophore Search. Molecular Modeling Studies
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3D database searching in drug design
inferredcites →https://doi.org/10.1021/jm00156a005openalex-snapshot
The ensemble approach to distance geometry: application to the nicotinic pharmacophore
inferredcites →https://doi.org/10.1021/jm00399a006openalex-snapshot
Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
inferredcites →https://doi.org/10.1073/pnas.90.8.3583openalex-snapshot
Structure-based inhibitor design by using protein models for the development of antiparasitic agents.
inferredcites →https://doi.org/10.1080/10629369508233998openalex-snapshot
Similarity Searching in Files of Three-Dimensional Structures: Evaluation of Similarity Coefficients and Standardisation Methods for Field-Based Similarity Searching
inferredcites →https://doi.org/10.1093/protein/6.7.723openalex-snapshot
Matching chemistry and shape in molecular docking
inferredcites →https://doi.org/10.1107/s0108270194010826openalex-snapshot
Hexaaquatitanium(III) Tris(p-Toluenesulfonate) Trihydrate
inferredcites →https://doi.org/10.1107/s0907444994011686openalex-snapshot
Correlation of binding affinities with non-bonded interaction energies of thrombin-inhibitor complexes
inferredcites →https://doi.org/10.1126/science.257.5073.1078openalex-snapshot
Structure-Based Strategies for Drug Design and Discovery
inferredcites →https://doi.org/10.1126/science.8278812openalex-snapshot
Rational Design of Potent, Bioavailable, Nonpeptide Cyclic Ureas as HIV Protease Inhibitors
inferredcites →https://doi.org/10.1126/science.8451640openalex-snapshot
Structure-Based Discovery of Inhibitors of Thymidylate Synthase
inferredcites →https://doi.org/10.1145/321921.321925openalex-snapshot
An Algorithm for Subgraph Isomorphism

What points at this work

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

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Three‐dimensional Structure Searching
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Applications of the Pharmacophore Concept in Natural Product inspired Drug Design
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Pharmacophore Modelling and Screening: Concepts, Recent Developments and Applications in Rational Drug Design
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The Pharmacophore Concept and Its Applications in Computer-Aided Drug Design
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Ligand-based drug design studies using predictive pharmacophore model generation on 4H-1,2,4-triazoles as AT1 receptor antagonists
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2/3D Pharmacophore Definitions and Their Application
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2/3D Pharmacophore definitions and their application
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Chapter 8. Antithrombotics/Serine Proteases
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Rational Combinatorial Library Design. 3. Simulated Annealing Guided Evaluation (SAGE) of Molecular Diversity: A Novel Computational Tool for Universal Library Design and Database Mining
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Three-Dimensional Pharmacophore Methods in Drug Discovery
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Do active site conformations of small ligands correspond to low free-energy solution structures?
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Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors
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Filtering databases and chemical libraries
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Filtering databases and chemical libraries
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A rapid identification of hit molecules for target proteins via physico-chemical descriptors
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Identification of potential CCR5 inhibitors through pharmacophore-based virtual screening, molecular dynamics simulation and binding free energy analysis
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A robust computational quest: Discovering potential hits to improve the treatment of pyrazinamide‐resistant Mycobacterium tuberculosis
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In silico identification of novel lead compounds with AT1 receptor antagonist activity: successful application of chemical database screening protocol
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Use of 3D Pharmacophore Models in 3D Database Searching
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Exploring the Mechanism and discovery of potential hits to improve the treatment of pyrazinamide-resistant Mycobacterium tuberculosis
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History and Evolution of the Pharmacophore Concept in Computer-Aided Drug Design
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Identification of 3-((1-(Benzyl(2-hydroxy-2-phenylethyl)amino)-1-oxo-3-phenylpropan-2-yl)carbamoyl)pyrazine-2-carboxylic Acid as a Potential Inhibitor of Non-Nucleosidase Reverse Transcriptase Inhibitors through InSilico Ligand- and Structure-Based Approaches
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Pharmacophore Models of Paclitaxel- and Epothilone-Based Microtubule Stabilizing Agents
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Molecular docking based design of Inhibitors for viral Non-Nucleosidase as potential anti-retroviral agents
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