Pharmacophore modelling: a forty year old approach and its modern synergies.

No abstract is available for this paper.

• Publication year

  2011

• Venue

  Current Medicinal Chemistry

• Publication date

  2011-05-31

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.2174/092986711795933669PMID 21568893
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Three-dimensional quantitative structure-selectivity relationships analysis guided rational design of a highly selective ligand for the cannabinoid receptor 2.

  2011cited by this paper
• Pharmacophore-based virtual screening.

  2011cited by this paper
• Pharmacophore modeling and applications in drug discovery: challenges and recent advances.

  2010cited by this paper
• Three-dimensional pharmacophore methods in drug discovery.

  2010cited by this paper
• PhDD: a new pharmacophore-based de novo design method of drug-like molecules combined with assessment of synthetic accessibility.

  2010cited by this paper
• Discovery of novel fibroblast growth factor receptor 1 kinase inhibitors by structure-based virtual screening.

  2010cited by this paper
• One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space

  2010cited by this paper
• Predicting Multiple Ligand Binding Modes Using Self-Consistent Pharmacophore Hypotheses

  2009cited by this paper
• Mimicking direct protein–protein and solvent-mediated interactions in the CDP-methylerythritol kinase homodimer: a pharmacophore-directed virtual screening approach

  2009cited by this paper
• Directed discovery of agents targeting the Met tyrosine kinase domain by virtual screening.

  2009cited by this paper
• Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation

  2009cited by this paper
• Combining docking with pharmacophore filtering for improved virtual screening

  2009cited by this paper
• Managing protein flexibility in docking and its applications.

  2009cited by this paper
• A dynamic target-based pharmacophoric model mapping the CD4 binding site on HIV-1 gp120 to identify new inhibitors of gp120-CD4 protein-protein interactions.

  2009cited by this paper
• Pharmacophore-guided lead optimization: the rational design of a non-zinc coordinating, sub-micromolar inhibitor of the botulinum neurotoxin serotype a metalloprotease.

  2009cited by this paper
• AutoShim: Empirically Corrected Scoring Functions for Quantitative Docking with a Crystal Structure and IC50 Training Data

  2008cited by this paper
• Towards more accurate pharmacophore modeling: Multicomplex-based comprehensive pharmacophore map and most-frequent-feature pharmacophore model of CDK2.

  2008cited by this paper
• Pharmacophore-based virtual screening.

  2008cited by this paper
• An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

  2008cited by this paper
• Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores

  2008cited by this paper
• Targets Looking for Drugs: A Multistep Computational Protocol for the Development of Structure-Based Pharmacophores and Their Applications for Hit Discovery

  2008cited by this paper
• Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering.

  2008cited by this paper
• Small Molecule Inhibitors Targeting HIV‐1 Reverse Transcriptase Dimerization

  2008cited by this paper
• Synergies of virtual screening approaches.

  2008cited by this paper
• Pharmacophore modeling and molecular docking led to the discovery of inhibitors of human immunodeficiency virus-1 replication targeting the human cellular aspartic acid-glutamic acid-alanine-aspartic acid box polypeptide 3.

  2008cited by this paper
• Discovery of multitarget inhibitors by combining molecular docking with common pharmacophore matching.

  2008cited by this paper
• 1-[(3-Aryloxy-3-aryl)propyl]-1H-imidazoles, new imidazoles with potent activity against Candida albicans and dermatophytes. Synthesis, structure-activity relationship, and molecular modeling studies.

  2008cited by this paper
• A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application

  2007cited by this paper
• High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening

  2007cited by this paper
• Structure-activity relationships in the binding of chemically derivatized CD4 to gp120 from human immunodeficiency virus.

  2007cited by this paper
• Target-based approach to inhibitors of histone arginine methyltransferases.

  2007cited by this paper
• Protein flexibility and species specificity in structure-based drug discovery: dihydrofolate reductase as a test system.

  2007cited by this paper
• Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure-Based Drug Discovery

  2007cited by this paper
• Molecular dynamics: survey of methods for simulating the activity of proteins.

  2006cited by this paper
• sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank

  2006cited by this paper
• Novel procedure for modeling ligand/receptor induced fit effects.

  2006cited by this paper
• Pocket v.2: Further Developments on Receptor-Based Pharmacophore Modeling

  2006cited by this paper
• GBPM: GRID-based pharmacophore model: concept and application studies to protein-protein recognition

  2006cited by this paper
• Refining the multiple protein structure pharmacophore method: consistency across three independent HIV-1 protease models.

  2006cited by this paper
• Possible dynamic anchor points in a benzoxazinone derivative–human oxytocin receptor system — a molecular docking and dynamics calculation

  2006cited by this paper
• Dynamic pharmacophore model optimization: identification of novel HIV-1 integrase inhibitors.

  2006cited by this paper
• Common pharmacophores for uncharged human ether-a-go-go-related gene (hERG) blockers.

  2006cited by this paper
• Development of a quasi-dynamic pharmacophore model for anti-complement peptide analogues.

  2005cited by this paper
• LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters

  2005cited by this paper
• GPCR Antitarget Modeling: Pharmacophore Models for Biogenic Amine Binding GPCRs to Avoid GPCR‐Mediated Side Effects

  2005cited by this paper
• Combining structure-based drug design and pharmacophores.

  2005cited by this paper
• Pharmacophore modeling, docking, and principal component analysis based clustering: combined computer-assisted approaches to identify new inhibitors of the human rhinovirus coat protein.

  2005cited by this paper
• Dynamic receptor-based pharmacophore model development and its application in designing novel HIV-1 integrase inhibitors.

  2005cited by this paper
• The Identification of Ligand Features Essential for PXR Activation by Pharmacophore Modeling

  2005cited by this paper
• Virtual Screening and Scaffold Hopping Based on GRID Molecular Interaction Fields

  2005cited by this paper
• A predictive pharmacophore model of human melanocortin-4 receptor as derived from the solution structures of cyclic peptides.

  2004cited by this paper
• Identification of compounds with nanomolar binding affinity for checkpoint kinase-1 using knowledge-based virtual screening.

  2004cited by this paper
• MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

  2004cited by this paper
• Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions.

  2004cited by this paper
• Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case.

  2004cited by this paper
• Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment

  2004cited by this paper
• Virtual Screening for SARS-CoV Protease Based on KZ7088 Pharmacophore Points

  2004cited by this paper
• Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design.

  2004cited by this paper
• The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.

  2003cited by this paper
• Pharmacophore‐based molecular docking to account for ligand flexibility

  2003cited by this paper
• Docking and database screening reveal new classes of Plasmodium falciparum dihydrofolate reductase inhibitors.

  2003cited by this paper
• Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis.

  2003cited by this paper
• Binding site characteristics in structure-based virtual screening: evaluation of current docking tools

  2003cited by this paper
• Pharmacophore discovery--lessons learned.

  2003cited by this paper
• Computational drug design accommodating receptor flexibility: the relaxed complex scheme.

  2002cited by this paper
• Protein flexibility and drug design: how to hit a moving target.

  2002cited by this paper
• Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation.

  2002cited by this paper
• Flexible docking under pharmacophore type constraints

  2002cited by this paper
• Pharmacophore modeling of cytochromes P450.

  2002cited by this paper
• Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors

  2000cited by this paper
• Developing a dynamic pharmacophore model for HIV-1 integrase.

  2000cited by this paper
• Molecular dynamics studies on the HIV-1 integrase catalytic domain.

  1999cited by this paper
• SuperStar: a knowledge-based approach for identifying interaction sites in proteins.

  1999cited by this paper
• Active-site-directed 3D database searching: Pharmacophore extraction and validation of hits

  1996cited by this paper
• A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists

  1993cited by this paper
• LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads

  1992cited by this paper
• The computer program LUDI: A new method for the de novo design of enzyme inhibitors

  1992cited by this paper
• Functionality maps of binding sites: A multiple copy simultaneous search method

  1991cited by this paper
• A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.

  1985cited by this paper

• Deciphering the inhibitory mechanisms of Interleukin-17A through dynamic molecular insights: a path toward novel anti-inflammatory therapies

  2025cites this paper
• From pharmacophore predictions to pharmaceutical possibilities: an integrated approach to screen M3 selective muscarinic receptor antagonist

  2025cites this paper
• Widely-targeted in silico and in vitro evaluation of veratrum alkaloid analogs as FAK inhibitors and dual targeting of FAK and Hh/SMO pathways for cancer therapy: A critical analysis.

  2024cites this paper
• Heat shock proteins as hallmarks of cancer: insights from molecular mechanisms to therapeutic strategies

  2024cites this paper
• POTENTIAL ACTIVITY OF KAEMPFEROL AS ANTI-PARKINSON’S; MOLECULAR DOCKING AND PHARMACOPHORE MODELLING STUDY

  2023cites this paper
• Artificial intelligence revolutionizing drug development: Exploring opportunities and challenges

  2023cites this paper
• MOLECULAR DOCKING STUDY AND PHARMACOPHORE MODELLING OF URSOLIC ACID AS AN ANTIMALARIAL USING STRUCTURE-BASED DRUG DESIGN METHOD

  2023cites this paper
• STRUCTURE-BASED DRUG DESIGN METHOD: MOLECULAR DOCKING STUDY AND PHARMACOPHORE MODELLING OF APIGENIN AS AN ANTIMALARIAL

  2023cites this paper
• Applications of the Novel Quantitative Pharmacophore Activity Relationship Method QPhAR in Virtual Screening and Lead-Optimisation

  2022cites this paper
• In Silico Drug Discovery for Treatment of Virus Diseases.

  2022cites this paper
• Drug Design by Pharmacophore and Virtual Screening Approach

  2022cites this paper
• Interface inhibitory action on Interleukin-1β using selected anti-inflammatory compounds to mitigate the depression: A computational investigation

  2022cites this paper
• Ligand- and Structure-Based Virtual Screening in Drug Discovery

  2021cites this paper
• 3D-PHARMACOPHORE MODELLING OF OMEGA-3 DERIVATIVES WITH PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA AS AN ANTI-OBESITY AGENT

  2021cites this paper
• Structure-based molecular modeling in SAR analysis and lead optimization

  2021cites this paper
• In Silico Modeling of Anticancer Drugs: Recent Advances

  2021cites this paper
• Pharmacophore Modeling in Drug Discovery: Methodology and Current Status

  2021cites this paper
• Recent developments and strategies for the discovery of TACE inhibitors

  2020cites this paper
• Virtual screening of small-molecule libraries

  2020cites this paper
• Appraisal of the role of In silico Methods in Pyrazole based drug design.

  2020cites this paper
• Identification of potential TNF-α inhibitors: from in silico to in vitro studies

  2020cites this paper
• From the Explored to the Unexplored: Computer-Tailored Drug Design Attempts in the Discovery of Selective Caspases Inhibitors.

  2019cites this paper
• ZIKA DRUG DISCOVERY-A REVIEW

  2019cites this paper
• Applications of Chemoinformatics in Drug Discovery

  2019cites this paper
• Development and Testing of Druglike Screening Libraries

  2018cites this paper
• Computational Modeling of Multi-target-Directed Inhibitors Against Alzheimer’s Disease

  2018cites this paper
• In Silico Chemogenomics Drug Repositioning Strategies for Neglected Tropical Diseases.

  2018cites this paper
• 2D and 3D structure–activity modelling of mosquito repellents: a review$

  2018cites this paper
• Computational drug discovery for the Zika virus

  2018cites this paper
• Discovery by organism based high-throughput screening of new multi-stage compounds affecting Schistosoma mansoni viability, egg formation and production

  2017cites this paper
• QSAR/QSPR Modeling in the Design of Drug Candidates with Balanced Pharmacodynamic and Pharmacokinetic Properties

  2017cites this paper
• Chalcone Derivatives: Promising Starting Points for Drug Design

  2017cites this paper
• Mechanistic Insights into the Binding of Class IIa HDAC Inhibitors toward Spinocerebellar Ataxia Type-2: A 3D-QSAR and Pharmacophore Modeling Approach

  2017influential citation
• LIGAND BASED PHARMACOPHORE MODELING, VIRTUAL SCREENING AND MOLECULAR DOCKING STUDIES TO DESIGN NOVEL PANCREATIC LIPASE INHIBITORS

  2017cites this paper
• Software and Web Resources for Computer-Aided Molecular Modeling and Drug Discovery

  2016cites this paper
• Pharmacological exploitation of the phenothiazine antipsychotics to develop novel antitumor agents–A drug repurposing strategy

  2016cites this paper
• Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise

  2016cites this paper
• Modern approaches to accelerate discovery of new antischistosomal drugs

  2016cites this paper
• Synopsis of Chemometric Applications to Model PPAR Agonism

  2016cites this paper
• Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015

  2016cites this paper
• Antioxidant properties of 5 herbal plants based ofpharmacophore modeling

  2016cites this paper
• Characterization of Centrally Expressed Solute Carriers : Histological and Functional Studies with Transgenic Mice

  2016cites this paper
• Accurate Prediction of Ligand Affinities for a Proton-Dependent Oligopeptide Transporter

  2016cites this paper
• SLC transporters as therapeutic targets: emerging opportunities

  2015cites this paper
• Natural Products as Leads in Schistosome Drug Discovery

  2015cites this paper
• Pharmacophore modeling for the identification of small-molecule inhibitors of TACE.

  2015cites this paper
• Latest advances in molecular topology applications for drug discovery

  2015cites this paper
• Identification and Validation Novel of VIM‐2 Metallo‐β‐lactamase Tripeptide Inhibitors

  2015cites this paper
• Discovery of a small-molecule inhibitor of STAT3 by ligand-based pharmacophore screening.

  2015cites this paper
• Docking and Pharmacophore Modelling for Virtual Screening

  2014cites this paper
• Hierarchical virtual screening approaches in small molecule drug discovery

  2014cites this paper
• An Unbiased Method To Build Benchmarking Sets for Ligand-Based Virtual Screening and its Application To GPCRs

  2014cites this paper
• A Pre-Docking Filter Based on Image Recognition

  2014cites this paper
• Virtual screening strategies in medicinal chemistry: the state of the art and current challenges.

  2014cites this paper
• Setting the Record Straight: The Origin of the Pharmacophore Concept

  2014cites this paper
• Medicinal Chemistry Approaches to Neglected Diseases Drug Discovery

  2014cites this paper
• Rational design of inhibitors of the bacterial cell wall synthetic enzyme GlmU using virtual screening and lead-hopping.

  2014cites this paper
• Recent advances in computer-aided drug design as applied to anti-influenza drug discovery.

  2014cites this paper
• Structure-based design of small-molecule protein-protein interaction modulators: the story so far.

  2014cites this paper
• Review Special FocuS: computational chemiStRy

  2014cites this paper
• Discovery of Natural Products that Modulate the Activity of PPARgamma: A Source for New Antidiabetics

  2014cites this paper
• Novel protein–protein interaction inhibitor of Nrf2–Keap1 discovered by structure-based virtual screening

  2014cites this paper
• Desenvolvimento de modelos de QSAR e análise quimioinformática da sensibilização e permeabilidade da pele

  2014cites this paper
• Foodinformatics: Applications of Chemical Information to Food Chemistry

  2014cites this paper
• Practical Chemoinformatics

  2014cites this paper
• Structure-based design of small-molecule protein – protein interaction modulators : the story

  2014cites this paper
• The role of 3D pharmacophore mapping based virtual screening for identification of novel anticancer agents: an overview.

  2013cites this paper
• Emerging Topics in Structure-Based Virtual Screening

  2013cites this paper
• Assessing the performance of 3D pharmacophore models in virtual screening: how good are they?

  2013cites this paper
• Pharmacophore modeling for ADME.

  2013cites this paper
• New in silico and conventional in vitro approaches to advance HIV drug discovery and design

  2013cites this paper
• In silico screening of quadruplex-binding ligands.

  2012cites this paper
• Physiologically based pharmacokinetic models: integration of in silico approaches with micro cell culture analogues.

  2012cites this paper
• Comparative Analysis of Pharmacophore Screening Tools

  2012cites this paper
• Structure and Ligand Based Drug Design Strategies in the Development of Novel 5-LOX Inhibitors

  2012cites this paper
• Pharmacophore modelling as a virtual screening tool for the discovery of small molecule protein-protein interaction inhibitors.

  2012cites this paper