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An Integrated Approach to Ligand- and Structure-Based Drug Design: Development and Application to a Series of Serine Protease Inhibitors

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

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Exhaustive docking of molecular fragments with electrostatic solvation
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3D‐QSAR Using the GRID/GOLPE Approach
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Integrated Approach Using Protein and Ligand Information to Analyze Selectivity‐ and Affinity‐Determining Features of Carbonic Anhydrase Isozymes
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A new implicit solvent model for protein–ligand docking
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Generating Optimal Linear PLS Estimations (GOLPE): An Advanced Chemometric Tool for Handling 3D‐QSAR Problems
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The Importance of Being Earnest: Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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Evaluation of reactant-based and product-based approaches to the design of combinatorial libraries
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The Design of Innovation
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3D-QSAR illusions
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A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers
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Geometry of binding of the Nα‐tosylated piperidides of m‐amidino‐, p‐amidino‐ and p‐guanidino phenylalanine to thrombin and trypsin
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Refined 2·3ÅX-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA
inferredcites →https://doi.org/10.1016/j.bmc.2005.02.027openalex-snapshot
3D-QSAR CoMFA studies on trypsin-like serine protease inhibitors: a comparative selectivity analysis
inferredcites →https://doi.org/10.1016/s0168-9525(00)02024-2openalex-snapshot
EMBOSS: The European Molecular Biology Open Software Suite
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Some recent developments in PLS modeling
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Automatic generation of alignments for 3D QSAR analyses
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Consensus scoring for ligand/protein interactions
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Virtual Screening against Highly Charged Active Sites: Identifying Substrates of Alpha−Beta Barrel Enzymes
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Evaluation of Binary QSAR Models Derived from LUDI and MOE Scoring Functions for Structure Based Virtual Screening
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Modeling Ligand−Receptor Interaction for Some MHC Class II HLA-DR4 Peptide Mimetic Inhibitors Using Several Molecular Docking and 3D QSAR Techniques
inferredcites →https://doi.org/10.1021/ci050293lopenalex-snapshot
QSAR and QSPR Studies of a Highly Structured Physicochemical Domain
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FLAME: A Program to Flexibly Align Molecules
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Screening of Matrix Metalloproteinases Available from the Protein Data Bank: Insights into Biological Functions, Domain Organization, and Zinc Binding Groups
inferredcites →https://doi.org/10.1021/ci700214jopenalex-snapshot
Homology Modeling and Receptor-Based 3D-QSAR Study of Carbonic Anhydrase IX
inferredcites →https://doi.org/10.1021/ci7002472openalex-snapshot
Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions
inferredcites →https://doi.org/10.1021/ja00226a005openalex-snapshot
Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
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Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
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A Novel Strategy for Improving Ligand Selectivity in Receptor-Based Drug Design
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Compass: Predicting Biological Activities from Molecular Surface Properties. Performance Comparisons on a Steroid Benchmark
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Comparative Molecular Field Analysis Using GRID Force-Field and GOLPE Variable Selection Methods in a Study of Inhibitors of Glycogen Phosphorylase b
inferredcites →https://doi.org/10.1021/jm000934yopenalex-snapshot
GRID/CPCA: A New Computational Tool To Design Selective Ligands
inferredcites →https://doi.org/10.1021/jm001028oopenalex-snapshot
Inhibition of Monoamine Oxidases by Functionalized Coumarin Derivatives: Biological Activities, QSARs, and 3D-QSARs
inferredcites →https://doi.org/10.1021/jm001070jopenalex-snapshot
Comparative Binding Energy (COMBINE) Analysis of Influenza Neuraminidase−Inhibitor Complexes
inferredcites →https://doi.org/10.1021/jm0011326openalex-snapshot
Suitability of Molecular Descriptors for Database Mining. A Comparative Analysis
inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
inferredcites →https://doi.org/10.1021/jm010894dopenalex-snapshot
Coumarins Derivatives as Dual Inhibitors of Acetylcholinesterase and Monoamine Oxidase
inferredcites →https://doi.org/10.1021/jm020919oopenalex-snapshot
Multiobjective Optimization in Quantitative Structure−Activity Relationships: Deriving Accurate and Interpretable QSARs
inferredcites →https://doi.org/10.1021/jm0304358openalex-snapshot
General Model for Estimation of the Inhibition of Protein Kinases Using Monte Carlo Simulations
inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot
Assessing Scoring Functions for Protein−Ligand Interactions
inferredcites →https://doi.org/10.1021/jm050436vopenalex-snapshot
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
inferredcites →https://doi.org/10.1021/jm060183lopenalex-snapshot
Structural Insights into Monoamine Oxidase Inhibitory Potency and Selectivity of 7-Substituted Coumarins from Ligand- and Target-Based Approaches
inferredcites →https://doi.org/10.1021/jm060350hopenalex-snapshot
Comparative Binding Energy Analysis Considering Multiple Receptors: A Step toward 3D-QSAR Models for Multiple Targets
inferredcites →https://doi.org/10.1021/jm070593popenalex-snapshot
A Flexible Approach to Induced Fit Docking
inferredcites →https://doi.org/10.1021/jm9608016openalex-snapshot
Smart Region Definition: A New Way To Improve the Predictive Ability and Interpretability of Three-Dimensional Quantitative Structure−Activity Relationships
inferredcites →https://doi.org/10.1021/jm981062ropenalex-snapshot
Three-Dimensional Quantitative Structure−Activity Relationship Analyses Using Comparative Molecular Field Analysis and Comparative Molecular Similarity Indices Analysis To Elucidate Selectivity Differences of Inhibitors Binding to Trypsin, Thrombin, and Factor Xa
inferredcites →https://doi.org/10.1023/a:1008797526431openalex-snapshot
Evaluation of reactant-based and product-based approaches to the design of combinatorial libraries
inferredcites →https://doi.org/10.1023/a:1016357811882openalex-snapshot
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
inferredcites →https://doi.org/10.1038/194178b0openalex-snapshot
Correlation of Biological Activity of Phenoxyacetic Acids with Hammett Substituent Constants and Partition Coefficients
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1515/bc.2002.130openalex-snapshot
(R)-3-Amidinophenylalanine-Derived Inhibitors of Factor Xa with a Novel Active-Site Binding Mode
inferredcites →https://doi.org/10.2174/1381612033454568openalex-snapshot
Pharmacophore Discovery - Lessons Learned
inferredcites →https://doi.org/10.2174/1567204052931177openalex-snapshot
Pharmacophore Discovery - Lessons Learned
inferredcites →https://doi.org/10.2174/156802606775193338openalex-snapshot
Computational Approaches to Model Ligand Selectivity in Drug Design

What points at this work

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

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ChemInform Abstract: An Integrated Approach to Lignad‐ and Structure‐Based Drug Design: Development and Application to a Series of Serine Protease Inhibitors.
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