Virtual screening strategies in medicinal chemistry: the state of the art and current challenges.

No abstract is available for this paper.

• Publication year

  2014

• Venue

  Current Topics in Medicinal Chemistry

• Publication date

  2014-07-31

• Fields of study

  Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.2174/1568026614666140929120749PMID 25262801
• 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.

• Tuning HERG out: antitarget QSAR models for drug development.

  2014cited by this paper
• Drug repositioning by structure-based virtual screening.

  2013cited by this paper
• How far can virtual screening take us in drug discovery?

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

  2013cited by this paper
• Discovery of new potential hits of Plasmodium falciparum enoyl-ACP reductase through ligand- and structure-based drug design approaches.

  2013cited by this paper
• Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening

  2013cited by this paper
• Drug discovery applications for KNIME: an open source data mining platform.

  2012cited by this paper
• Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

  2012cited by this paper
• In silico Prediction of Chemical Ames Mutagenicity

  2012cited by this paper
• DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets

  2012cited by this paper
• Virtual screening methods as tools for drug lead discovery from large chemical libraries.

  2012cited by this paper
• ZINC: A Free Tool to Discover Chemistry for Biology

  2012cited by this paper
• Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures

  2012cited by this paper
• Structural and chemical basis for enhanced affinity to a series of mycobacterial thymidine monophosphate kinase inhibitors: fragment-based QSAR and QM/MM docking studies

  2012cited by this paper
• Freely accessible databases of commercial compounds for high- throughput virtual screenings.

  2012cited by this paper
• A Bayesian Approach to in Silico Blood-Brain Barrier Penetration Modeling

  2012cited by this paper
• Amphotericin primarily kills yeast by simply binding ergosterol

  2012cited by this paper
• Macrolides: the plug is out.

  2012cited by this paper
• FRED and HYBRID docking performance on standardized datasets

  2012cited by this paper
• Freely accessible databases of commercial compounds for high- throughput virtual screenings.

  2012cited by this paper
• ChEMBL: a large-scale bioactivity database for drug discovery

  2011cited by this paper
• Advances in automated NMR protein structure determination

  2011cited by this paper
• Outstanding challenges in protein–ligand docking and structure‐based virtual screening

  2011cited by this paper
• Predicting drug-induced hepatotoxicity using QSAR and toxicogenomics approaches.

  2011cited by this paper
• Integration of virtual and high throughput screening in lead discovery settings.

  2011cited by this paper
• Impact of high-throughput screening in biomedical research

  2011cited by this paper
• Evaluating the effect of unbalanced data in biomedical document classification

  2011cited by this paper
• FRED Pose Prediction and Virtual Screening Accuracy

  2011cited by this paper
• State-of-the-art in ligand-based virtual screening.

  2011cited by this paper
• PubChem's BioAssay Database

  2011cited by this paper
• AUC-RF: A New Strategy for Genomic Profiling with Random Forest

  2011cited by this paper
• Open Babel: An open chemical toolbox

  2011cited by this paper
• Random forests ensemble classifier trained with data resampling strategy to improve cardiac arrhythmia diagnosis

  2011cited by this paper
• Pharmacophore modelling: a forty year old approach and its modern synergies.

  2011cited by this paper
• Binary Classification of Aqueous Solubility Using Support Vector Machines with Reduction and Recombination Feature Selection

  2011cited by this paper
• The problems with today's pharmaceutical business—an outsider's view

  2011cited by this paper
• A unified, probabilistic framework for structure- and ligand-based virtual screening.

  2011cited by this paper
• An active learning based classification strategy for the minority class problem: application to histopathology annotation

  2011cited by this paper
• How Do 2D Fingerprints Detect Structurally Diverse Active Compounds? Revealing Compound Subset-Specific Fingerprint Features through Systematic Selection

  2011cited by this paper
• A New approach for Classification of Highly Imbalanced Datasets using Evolutionary Algorithms

  2011cited by this paper
• Understanding drug‐likeness

  2011cited by this paper
• Structure-based prediction and biosynthesis of the major mammalian metabolite of the cardioactive prototype LASSBio-294.

  2010cited by this paper
• Best Practices for QSAR Model Development, Validation, and Exploitation

  2010cited by this paper
• Working to overcome the global impact of neglected tropical diseases : first WHO report on neglected tropical diseases

  2010cited by this paper
• Extended-Connectivity Fingerprints

  2010cited by this paper
• Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

  2010cited by this paper
• 3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents

  2010cited by this paper
• Structural Characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei Bound to the Antifungal Drugs Posaconazole and Fluconazole

  2010cited by this paper
• Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research

  2010cited by this paper
• Quo vadis, virtual screening? A comprehensive survey of prospective applications.

  2010cited by this paper
• Advances in Chagas disease drug development: 2009–2010

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

  2010cited by this paper
• Pharmacophore modeling and applications in drug discovery: challenges and recent advances.

  2010cited by this paper
• Structural Insights into Inhibition of Sterol 14α-Demethylase in the Human Pathogen Trypanosoma cruzi*

  2010cited by this paper
• Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods

  2010cited by this paper
• Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

  2010cited by this paper
• Virtual screening: an endless staircase?

  2010cited by this paper
• An overview of the PubChem BioAssay resource

  2009cited by this paper
• Ergosterol biosynthesis and drug development for Chagas disease.

  2009cited by this paper
• Bmc Medical Research Methodology Open Access a Multivariate Hierarchical Bayesian Approach to Measuring Agreement in Repeated Measurement Method Comparison Studies

  2009cited by this paper
• Current epidemiological trends for Chagas disease in Latin America and future challenges in epidemiology, surveillance and health policy.

  2009cited by this paper
• The Effect of Ligand-Based Tautomer and Protomer Prediction on Structure-Based Virtual Screening

  2009cited by this paper
• Machine learning in virtual screening.

  2009cited by this paper
• How not to develop a quantitative structure–activity or structure–property relationship (QSAR/QSPR)

  2009cited by this paper
• Docking screens: right for the right reasons?

  2009cited by this paper
• Application of Random Forest Approach to QSAR Prediction of Aquatic Toxicity

  2009cited by this paper
• Molecular mechanisms of Trypanosoma cruzi infection by oral route.

  2009cited by this paper
• Targeted scoring functions for virtual screening.

  2009cited by this paper
• Analysis of the Calculated Physicochemical Properties of Respiratory Drugs: Can We Design for Inhaled Drugs Yet?

  2009cited by this paper
• Rational Design and 3D-Pharmacophore Mapping of 5′-Thiourea-Substituted α-Thymidine Analogues as Mycobacterial TMPK Inhibitors

  2009cited by this paper
• AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

  2009cited by this paper
• Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?

  2008cited by this paper
• Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results

  2008cited by this paper
• Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?

  2008cited by this paper
• Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping

  2008cited by this paper
• Recommendations for evaluation of computational methods

  2008cited by this paper
• What do we know and when do we know it?

  2008cited by this paper
• Fragment-based and classical quantitative structure–activity relationships for a series of hydrazides as antituberculosis agents

  2008cited by this paper
• Community benchmarks for virtual screening

  2008cited by this paper
• Abordagem racional no planejamento de novos tuberculostáticos: inibidores da InhA, enoil-ACP redutase do M. tuberculosis

  2008cited by this paper
• Three-Dimensional Quantitative Structure-Activity Relationships for a Large Series of Potent Antitubercular Agents

  2008cited by this paper
• Bias, reporting, and sharing: computational evaluations of docking methods

  2008cited by this paper
• Evaluating Virtual Screening Methods: Good and Bad Metrics for the "Early Recognition" Problem

  2007cited by this paper
• Efficient overlay of small organic molecules using 3D pharmacophores

  2007cited by this paper
• Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches.

  2007cited by this paper
• A new descriptor selection scheme for SVM in unbalanced class problem: a case study using skin sensitisation dataset

  2007cited by this paper
• Posaconazole: an extended-spectrum triazole antifungal agent.

  2007cited by this paper
• Docking and scoring--theoretically easy, practically impossible?

  2006cited by this paper
• Evaluation of the chemiluminescent nitrogen detector for solubility determinations to support drug discovery.

  2006cited by this paper
• Novel 2D Fingerprints for Ligand-Based Virtual Screening

  2006cited by this paper
• Consensus scoring for protein-ligand interactions.

  2006cited by this paper
• Benchmarking sets for molecular docking.

  2006cited by this paper
• Virtual ligand screening: strategies, perspectives and limitations

  2006cited by this paper
• Circular fingerprints: flexible molecular descriptors with applications from physical chemistry to ADME.

  2006cited by this paper
• BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities

  2006cited by this paper
• Cost curves: An improved method for visualizing classifier performance

  2006cited by this paper
• High-Throughput Calculation of Protein-Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing

  2006cited by this paper
• Use of an Induced Fit Receptor Structure in Virtual Screening

  2006cited by this paper
• Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: ranking, voting, and consensus scoring.

  2006cited by this paper
• Posterior probability support vector Machines for unbalanced data

  2005cited by this paper

• System biology and network-based approach to identify the therapeutic signatures and potential inhibitors against polycystic lipomembranous osteodysplasia with Sclerosing Leukoencephalopathy.

  2026cites this paper
• TEMPORARY REMOVAL: Machine Learning-Driven Prediction of Corrosion Inhibition Efficiency on Copper: Incorporating Tautomer Stability and Virtual Screening for Inhibitor Repositioning

  2025cites this paper
• Recent advances in medicinal chemistry strategies for the development of METTL3 inhibitors.

  2025cites this paper
• DTBA-net: Drug-Target Binding Affinity prediction using feature selection in hybrid CNN model

  2025cites this paper
• Prediction and Prioritisation of Novel Anthelmintic Candidates from Public Databases Using Deep Learning and Available Bioactivity Data Sets

  2025cites this paper
• Novel drug discovery approaches for MMP-13 inhibitors in the treatment of osteoarthritis.

  2024cites this paper
• Enhanced Protein-Ligand Affinity Prediction with Conditional Updating and Proximity Embedding

  2024cites this paper
• Decoding Drug Discovery: Exploring A-to-Z In Silico Methods for Beginners

  2024cites this paper
• In Silico Therapeutic Study: The Next Frontier in the Fight against SARS-CoV-2 and Its Variants

  2024cites this paper
• Artificial intelligence-guided approach for efficient virtual screening of hits against Schistosoma mansoni.

  2023cites this paper
• Advances in machine intelligence‐driven virtual screening approaches for big‐data

  2023cites this paper
• Modeling and analysis of ensemble average solvation energy and solute-solvent interfacial fluctuations

  2023cites this paper
• Affinity prediction using deep learning based on SMILES input for D3R grand challenge 4

  2022cites this paper
• QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis

  2022cites this paper
• The Structure of Biologically Active Functionalized Azoles: NMR Spectroscopy and Quantum Chemistry

  2022cites this paper
• The Structure of Biologically Active Functionalized Azoles: NMR Spectroscopy and Quantum Chemistry

  2022cites this paper
• First In Silico Screening of Insect Molecules for Identification of Novel Anti-Parasitic Compounds

  2022cites this paper
• Tautomeric Conflicts in Forty Small-Molecule Databases

  2021cites this paper
• Best Practices for Docking-Based Virtual Screening

  2021cites this paper
• Structural analysis of dexrazoxane: Exploring tautomeric conformations

  2021cites this paper
• Commercial SARS-CoV-2 Targeted, Protease Inhibitor Focused and Protein–Protein Interaction Inhibitor Focused Molecular Libraries for Virtual Screening and Drug Design

  2021cites this paper
• Part-II- in silico drug design: application and success

  2021cites this paper
• In silico screening of anti-inflammatory constituents with good drug-like properties from twigs of Cinnamomum cassia based on molecular docking and network pharmacology

  2021cites this paper
• Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence

  2021cites this paper
• A Multi-Objective Approach for Anti-Osteosarcoma Cancer Agents Discovery through Drug Repurposing

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

  2020cites this paper
• Deep Learning-driven research for drug discovery: Tackling Malaria

  2020cites this paper
• In silico Strategies to Support Fragment-to-Lead Optimization in Drug Discovery

  2020cites this paper
• Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction

  2020cites this paper
• Bisbenzylisoquinoline alkaloids and P-glycoprotein function: A structure activity relationship study.

  2020cites this paper
• DeepAtom: A Framework for Protein-Ligand Binding Affinity Prediction

  2019cites this paper
• The Light and Dark Sides of Virtual Screening: What Is There to Know?

  2019cites this paper
• Virtual Screening Techniques in Drug Discovery: Review and Recent Applications.

  2019cites this paper
• Classification of Staphylococcus Aureus FabI Inhibitors by Machine Learning Techniques

  2019cites this paper
• Ligand based virtual screening using SVM on GPU

  2019cites this paper
• Impact of the Polymorphic Form of Drugs/ NCE s on Preformulation and Formulation Development

  2019cites this paper
• INACTIVATION OF CU-ZN SUPEROXIDE DISMUTASE OF MYCOBACTERIUM TUBERCULOSIS H37RV

  2019cites this paper
• STRUCTURE BASED DRUG DESIGN OF HIGH AFFINITY KRAS INHIBITORS

  2018cites this paper
• Convolutional neural network scoring and minimization in the D3R 2017 community challenge

  2018cites this paper
• Targeting thioredoxin glutathione reductase as a potential antischistosomal drug target.

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

  2018cites this paper
• Novel chemical scaffolds against Schistosoma mansoni discovered by combi-QSAR, virtual screening, and confirmed by experimental evaluation with automated imaging

  2018cites this paper
• The potential role of in silico approaches to identify novel bioactive molecules from natural resources.

  2017cites this paper
• QSAR-driven design, synthesis and discovery of potent chalcone derivatives with antitubercular activity.

  2017cites this paper
• Overview of Methods and Strategies for Conducting Virtual Small Molecule Screening

  2017cites this paper
• Identification of steroid-like natural products as antiplasmodial agents by 2D and 3D similarity-based virtual screening.

  2017cites this paper
• Targeting CYP51 for drug design by the contributions of molecular modeling

  2017cites this paper
• Discovery of Cdc25A Lead Inhibitors with a Novel Chemotype by Virtual Screening: Application of Pharmacophore Modeling Based on a Training Set with a Limited Number of Unique Components

  2017cites this paper
• Performance of a docking/molecular dynamics protocol for virtual screening of nutlin-class inhibitors of Mdmx.

  2017cites this paper
• QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni

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

  2016cites this paper
• Evaluation of cytotoxic effect of the combination of a pyridinyl carboxamide derivative and oxaliplatin on NCI-H1299 human non-small cell lung carcinoma cells.

  2016cites this paper
• Use of machine learning approaches for novel drug discovery

  2016cites this paper
• Discovery of New Anti-Schistosomal Hits by Integration of QSAR-Based Virtual Screening and High Content Screening.

  2016cites this paper
• Plate-based diversity subset screening generation 2: an improved paradigm for high-throughput screening of large compound files

  2016cites this paper
• A medicinal chemistry approach to drug repositioning in the treatment of tuberculosis and malaria

  2016cites this paper
• Small-Molecule Inhibitors of Protein–Protein Interactions

  2016cites this paper
• A Novel Diphenylthiosemicarbazide Is a Potential Insulin Secretagogue for Anti-Diabetic Agent

  2016cites this paper
• Natural Products as Leads in Schistosome Drug Discovery

  2015influential citation
• QSAR and Molecular Modeling Approaches for Prediction of Drug Metabolism

  2015cites this paper
• In Silico Repositioning-Chemogenomics Strategy Identifies New Drugs with Potential Activity against Multiple Life Stages of Schistosoma mansoni

  2015cites this paper
• Development of QSAR Models for Identification of CYP3A4 Substrates and Inhibitors

  2015cites this paper
• Computational allosteric ligand binding site identification on Ras proteins.

  2015cites this paper
• Strategies for the Discovery of Target-Specific or Isoform-Selective Modulators.

  2015cites this paper
• Insights into the Development of Chemotherapeutics Targeting PFKFB Enzymes

  2015cites this paper
• Tuning HERG out: antitarget QSAR models for drug development.

  2014cites this paper