FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects

BackgroundDrug discovery and chemical biology are exceedingly complex and demanding enterprises. In recent years there are been increasing awareness about the importance of predicting/optimizing the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of small chemical compounds along the search process rather than at the final stages. Fast methods for evaluating ADMET properties of small molecules often involve applying a set of simple empirical rules (educated guesses) and as such, compound collections' property profiling can be performed in silico. Clearly, these rules cannot assess the full complexity of the human body but can provide valuable information and assist decision-making.ResultsThis paper presents FAF-Drugs2, a free adaptable tool for ADMET filtering of electronic compound collections. FAF-Drugs2 is a command line utility program (e.g., written in Python) based on the open source chemistry toolkit OpenBabel, which performs various physicochemical calculations, identifies key functional groups, some toxic and unstable molecules/functional groups. In addition to filtered collections, FAF-Drugs2 can provide, via Gnuplot, several distribution diagrams of major physicochemical properties of the screened compound libraries.ConclusionWe have developed FAF-Drugs2 to facilitate compound collection preparation, prior to (or after) experimental screening or virtual screening computations. Users can select to apply various filtering thresholds and add rules as needed for a given project. As it stands, FAF-Drugs2 implements numerous filtering rules (23 physicochemical rules and 204 substructure searching rules) that can be easily tuned.

• Publication year

  2008

• Venue

  BMC Bioinformatics

• Publication date

  2008-09-24

• Fields of study

  Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1186/1471-2105-9-396PMID 18816385PMCID 2561050
• 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.

• Structure-Function Analyses of Single Nucleotide Polymorphisms in Human N-Acetyltransferase 1

  2008cited by this paper
• Role of hydrazine in isoniazid-induced hepatotoxicity in a hepatocyte inflammation model.

  2008cited by this paper
• Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

  2008cited by this paper
• Possible role of hydroxylated metabolites of tacrine in drug toxicity and therapy of Alzheimer's disease.

  2008cited by this paper
• Renal deterioration caused by carcinogens as a consequence of free radical mediated tissue damage: a review of the protective action of melatonin

  2007cited by this paper
• Aromatic Amines in Experimental Cancer Research: Tissue-Specific Effects, an Old Problem and New Solutions

  2007cited by this paper
• DrugBank: a knowledgebase for drugs, drug actions and drug targets

  2007cited by this paper
• An Empirical Process for the Design of High-Throughput Screening Deck Filters

  2006cited by this paper
• Bioactivation and hepatotoxicity of nitroaromatic drugs.

  2006cited by this paper
• FAF-Drugs: free ADME/tox filtering of compound collections

  2006influential reference
• Assessment of chemical libraries for their druggability

  2005cited by this paper
• DrugBank: a comprehensive resource for in silico drug discovery and exploration

  2005cited by this paper
• Cytochrome P450 activation of arylamines and heterocyclic amines.

  2005cited by this paper
• Characterisation of metabolites of the putative cancer chemopreventive agent quercetin and their effect on cyclo-oxygenase activity

  2004cited by this paper
• In silico prediction of ADME properties: are we making progress?

  2004cited by this paper
• Drug research: myths, hype and reality

  2003cited by this paper
• Nonleadlikeness and leadlikeness in biochemical screening.

  2003cited by this paper
• A specific mechanism of nonspecific inhibition.

  2003cited by this paper
• Identification and prediction of promiscuous aggregating inhibitors among known drugs.

  2003cited by this paper
• Profiling drug-like properties in discovery research.

  2003cited by this paper
• Molecular properties that influence the oral bioavailability of drug candidates.

  2002influential reference
• The emerging importance of predictive ADME simulation in drug discovery.

  2002cited by this paper
• A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening.

  2002cited by this paper
• Development of a virtual screening method for identification of "frequent hitters" in compound libraries.

  2002cited by this paper
• Structure-based virtual screening: an overview.

  2002cited by this paper
• Is There a Difference between Leads and Drugs? A Historical Perspective

  2001cited by this paper
• Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings.

  2001influential reference
• Calculating partition coefficient by atom-additive method

  2000cited by this paper
• Property distribution of drug-related chemical databases*

  2000cited by this paper
• Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties.

  2000cited by this paper
• Prediction of drug absorption using multivariate statistics.

  2000cited by this paper
• Prediction of Physicochemical Parameters by Atomic Contributions

  1999cited by this paper
• The Design of Leadlike Combinatorial Libraries.

  1999cited by this paper
• Nitroarene reduction and generation of free radicals by cell-free extracts of wild-type, and nitroreductase-deficient and -enriched Salmonella typhimurium strains used in the umu gene induction assay.

  1999cited by this paper
• Strategic Pooling of Compounds for High-Throughput Screening

  1999cited by this paper
• Properties of known drugs. 2. Side chains.

  1999cited by this paper
• Reactive compounds and in vitro false positives in HTS

  1997cited by this paper

• A Review of Automated Workflow Pipelines for Computational Chemists

  2025cites this paper
• Innovative computational approaches in drug discovery and design.

  2025cites this paper
• PROPRIEDADES FÍSICO-QUÍMICAS, FARMACOCINÉTICAS E APLICAÇÕES BIOMÉDICAS DO FITOCANABINÓIDE CANABIGEROL

  2025cites this paper
• A high throughput, high content screen for non-toxic small molecules that reduce levels of the nuclear lamina protein, Lamin B1

  2025cites this paper
• Computational biochemistry-guided discovery of novel Glycosidic inhibitors for human sodium-glucose transporter 2

  2025cites this paper
• Novel 2-substituted benzothiazole derivatives: synthesis, in vitro and in silico evaluations as potential anticancer agents

  2025cites this paper
• Computational assessment of the toxicological profiles of various chemicals to which humans are exposed. A review

  2024cites this paper
• Structural insights into the potential binding sites of Cathepsin D using molecular modelling techniques

  2024cites this paper
• Novel Schiff base derivatives containing 4,5-disubstituted thiazole as potential antibiofilm, anti-inflammatory and antioxidant agents: Green Synthesis, Molecular Docking and ADME analysis

  2024cites this paper
• Molecular Docking, ADME and Toxicity Study of Dibenzo-α-pyrone derivatives for GABA and NMDA receptors for their antiepileptic activity

  2024cites this paper
• Discovery of Non-Peptide GLP-1 Positive Allosteric Modulators from Natural Products: Virtual Screening, Molecular Dynamics, ADMET Profiling, Repurposing, and Chemical Scaffolds Identification

  2024cites this paper
• In the pursuit of novel therapeutic agents: synthesis, anticancer evaluation, and physicochemical insights of novel pyrimidine-based 2-aminobenzothiazole derivatives

  2024cites this paper
• Ultra-high throughput-based screening for the discovery of antiplatelet drugs affecting receptor dependent calcium signaling dynamics

  2024cites this paper
• Targeting NUDT5 For Breast Cancer Therapy: In-Silico Identification of Potent Inhibitors From Terminalia chebula

  2024cites this paper
• Comprehensive analysis of Seriphidium kurramense: GC/MS profiling, antibacterial and antibiofilm activities, molecular docking study and in-silico ADME profiling

  2024cites this paper
• Drug repurposing approach for potential Pfmrk inhibitors as antimalarial agents: an In-silico analysis

  2023cites this paper
• Antimalarial Agents Targeting Plasmodium falciparum Carbonic Anhydrase: Towards Artesunate Hybrid Compounds with Dual Mechanism of Action

  2023cites this paper
• Focusing on the moderately active compound (MAC) in the design and development of strategies to optimize the apoptotic effect by molecular mechanics techniques

  2023cites this paper
• Evaluation of Free Online ADMET Tools for Academic or Small Biotech Environments

  2023cites this paper
• A Schiff Base with Polymorphic Structure (Z′ = 2): Investigations with Computational Techniques and in Silico Predictions

  2023cites this paper
• Discovery of RC-752, a Novel Sigma-1 Receptor Antagonist with Antinociceptive Activity: A Promising Tool for Fighting Neuropathic Pain

  2023cites this paper
• Matrix‐Metalloproteinase Inhibitory Study of Novel Tetrahydroisoquinoline‐4‐carboxylates: Design, Synthesis, and Molecular Docking Studies

  2023cites this paper
• Novel S1R agonists counteracting NMDA excitotoxicity and oxidative stress: A step forward in the discovery of neuroprotective agents.

  2023cites this paper
• Molecular Dynamic Simulation Approach to Predict the Compatibility of Formulation Components of Salbutamol Sulfate Metered Dose Inhaler Free off Ethanol

  2023cites this paper
• Synthesis, Structural Elucidation, Physico-chemical Quantum Properties and In Silico Interaction Analysis of 2-methyl-3-((4-nitrobenzyl)oxy)quinoxaline

  2023cites this paper
• In Silico Exploration of PTP1B Inhibitor from Indole Alkaloids of Rauvolfia serpentina (L.) Benth, a Potent Therapeutic Drug Target for Type 2 Diabetes Mellitus

  2023cites this paper
• The reconciliation between the experimental and calculated octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using atomistic molecular dynamics: an open question

  2023influential citation
• Synthesis, Physicochemical Properties and Molecular Docking of New Benzothiazole Derivatives as Antimicrobial Agents Targeting DHPS Enzyme

  2022cites this paper
• A drug repurposing endeavor to discover a multi-targeting ligand against RhlR and LasR proteins from opportunistic human pathogen Pseudomonas aeruginosa

  2022cites this paper
• A single-molecule with multiple investigations: Synthesis, characterization, computational methods, inhibitory activity against Alzheimer's disease, toxicity, and ADME studies

  2022cites this paper
• QSAR Regression Models for Predicting the Activity of Inhibitors of Staphylococcus Epidermidis

  2022cites this paper
• Synthesis of Unsymmetrical Squaramides as Allosteric GSK‐3β Inhibitors Promoting β‐Catenin‐Mediated Transcription of TCF/LEF in Retinal Pigment Epithelial Cells

  2022cites this paper
• Design, molecular modeling, synthesis and biological evaluation of novel pyrazole based schiff Bases as fungal biofilm inhibitors

  2022cites this paper
• Synthesis, characterization, Hirshfeld surface analysis and molecular docking studies of 3-(cyclohexylthio)-4-hydroxy-6-methyl-2H-chromen-2-one

  2022cites this paper
• Synthesis, spectroscopic characterization, crystal structure, theoretical (DFT) studies and molecular docking analysis of biologically potent isopropyl 5-chloro-2-hydroxy-3-oxo-2,3-dihydrobenzofuran-2-carboxylate

  2022cites this paper
• Assessment of FDA-Approved Drugs as a Therapeutic Approach for Niemann-Pick Disease Type C1 Using Patient-Specific iPSC-Based Model Systems

  2022cites this paper
• The Synthesis of Triazolium Salts as Antifungal Agents: A Biological and In Silico Evaluation

  2022cites this paper
• Jumping from Fragment to Drug via Smart Scaffolds

  2022cites this paper
• A review of approaches in computer-aided drug design in drug discovery

  2022cites this paper
• Crystallographic structure, quantum and in silico interaction analysis of 3-(benzylthio)-4-hydroxy-2H-chromen-2-one

  2022cites this paper
• Synthesis, molecular docking, and preliminary cytotoxicity study of some novel 2-(naphthalen-1-yl)-methylimidazo[2,1-b][1,3,4]thiadiazoles

  2021cites this paper
• Virtual Screening of Natural Compounds Targeting Proteases of Coronaviruses and Picornaviruses

  2021cites this paper
• Synthesis, Characterization, Crystal Structure, Molecular Docking Analysis and Other Physico-Chemical Properties of (E)-2-(3,4-Dimethoxystyryl)Quinoline

  2021cites this paper
• Geraniol and Citral as potential therapeutic agents targeting the HSP90 activity: An in silico and experimental approach.

  2021cites this paper
• Investigating Fungi-Derived Bioactive Molecules as Inhibitor of the SARS Coronavirus Papain Like Protease: Computational Based Study

  2021cites this paper
• Identification of N,N-arylalkyl-picolinamide derivatives targeting the RNA-binding protein HuR, by combining biophysical fragment-screening and molecular hybridization.

  2021cites this paper
• Recent Advances in the Prediction of Pharmacokinetics Properties in Drug Design Studies: A Review

  2021cites this paper
• Natural Products-based drug design from Bahia Semi-Arid region against SARS-CoV-2 Mpro (3Clpro)

  2021cites this paper
• Molecular docking and simulation studies of flavonoid compounds against PBP-2a of methicillin‐resistant Staphylococcus aureus

  2021cites this paper
• Discovery of novel hit compounds as potential HDAC1 inhibitors: The case of ligand- and structure-based virtual screening

  2021cites this paper
• Computational Modeling of Chloroquine Analogues for Development of Drugs Against Novel Coronavirus (nCoV)

  2021cites this paper
• Natural Products-Based Drug Design against SARS-CoV-2 Mpro 3CLpro

  2021cites this paper
• Discovery of pyrrole derivatives for the treatment of glioblastoma and chronic myeloid leukemia.

  2021cites this paper
• 1,3-Dipolar cycloaddition, HPLC enantioseparation and docking studies of saccharin/isoxazole and saccharin/isoxazoline derivatives as selective carbonic anhydrase IX and XII inhibitors.

  2020cites this paper
• The Application of Negative Design to Design More Desirable Virtual Screening Library.

  2020cites this paper
• Virtual Screening and Bioactivity Evaluation of Novel Androgen Receptor Antagonists From Anti-PCa Traditional Chinese Medicine Prescriptions

  2020cites this paper
• Computational investigation for identification of potential phytochemicals and antiviral drugs as potential inhibitors for RNA-dependent RNA polymerase of COVID-19

  2020cites this paper
• Inhibition of multidrug resistance property of Candida albicans by natural compounds of parthenium hysterophorus L. An In-Silico approach

  2020cites this paper
• Systematic evaluation of the mechanisms of Mulberry leaf (Morus alba Linne) acting on diabetes based on network pharmacology and molecular docking.

  2020cites this paper
• Molecular Docking-based Virtual Screening, Molecular Dynamics and Atoms in Molecules (AIM) Studies to Identify Potential Inhibitor against the Extracellular Region of Human Epidermal Receptor 2

  2020cites this paper
• Synthesis, structural, spectral and antibacterial activity of 3,3a,4,5-tetrahydro-2H-benzo[g]indazole fused carbothioamide derivatives as antibacterial agents

  2020cites this paper
• Frequent hitters: nuisance artifacts in high-throughput screening.

  2020cites this paper
• Strategies of Virtual Screening in Medicinal Chemistry

  2020cites this paper
• Ligand-based Drug Design Approach in Designing New Leads from Existing Pharmacophores; Binding Pocket Estimation and Binding Pocket-directed Screening of Antiviral Drugs for Treatment of Novel Corona COVID-19 and Topoisomerase Inhibitors

  2020cites this paper
• Expanding the anticancer potential of 1,2,3-triazoles via simultaneously targeting Cyclooxygenase-2, 15-lipoxygenase and tumor-associated carbonic anhydrases.

  2020cites this paper
• Structure-based design, semi-synthesis and anti-inflammatory activity of tocotrienolic amides as 5-lipoxygenase inhibitors.

  2020cites this paper
• Pyridine and Benzoisothiazole Decorated Vanillin Chalcones: Synthesis, Antimicrobial, Antioxidant, Molecular docking and ADMET study.

  2020cites this paper
• Synthesis and Biological Evaluation of Carvacrol-Based Derivatives as Dual Inhibitors of H. pylori Strains and AGS Cell Proliferation

  2020cites this paper
• In Silico identification of potential drug targets by subtractive genome analysis of Enterococcus faecium DO

  2020cites this paper
• Computational Approaches to Evaluate Ecotoxicity of Biocides: Cases from the Project COMBASE

  2020cites this paper
• Synthesis, docking and in vitro evaluation of -proline derived 1,3-diketones possessing anti-cancer and anti-inflammatory activities

  2020cites this paper
• Discovery of potential species-specific green insecticides targeting lepidopteran ryanodine receptor.

  2020cites this paper
• New N‐phenylacetamide‐linked 1,2,3‐triazole‐tethered coumarin conjugates: Synthesis, bioevaluation, and molecular docking study

  2020cites this paper
• In silico identification and evaluation of new Trypanosoma cruzi trypanothione reductase (TcTR) inhibitors obtained from natural products database of the Bahia semi-arid region (NatProDB)

  2019cites this paper
• Benzoic acid-derived nitrones: A new class of potential acetylcholinesterase inhibitors and neuroprotective agents.

  2019cites this paper
• Rationalization of a traditional liver medicine using systems biology approach and its evaluation in preclinical trial

  2019cites this paper
• Identification of dual site inhibitors of tankyrase through virtual screening of protein-ligand interaction fingerprint (PLIF)–derived pharmacophore models, molecular dynamics, and ADMET studies

  2019cites this paper
• Dehydrodieugenol B derivatives as antiparasitic agents: Synthesis and biological activity against Trypanosoma cruzi.

  2019cites this paper
• Discovery of novel substituted N-(6-Chloro-3-cyano-4-phenyl-4H-chromen-2-yl)-2-(4-chloro-phenoxy)-acetamide for biphasic anticancer and anticonvulsant activities.

  2019cites this paper
• 5-Arylidene(chromenyl-methylene)-thiazolidinediones: Potential New Agents against Mutant Oncoproteins K-Ras, N-Ras and B-Raf in Colorectal Cancer and Melanoma

  2019cites this paper
• Design and Synthesis of Novel Inhibitor against Ser121 and Val122 Mutations in P53 Cancer Gene

  2019cites this paper
• Molecular docking, pharmacophore based virtual screening and molecular dynamics studies towards the identification of potential leads for the management of H. pylori

  2019cites this paper
• South African Abietane Diterpenoids and Their Analogs as Potential Antimalarials: Novel Insights from Hybrid Computational Approaches

  2019cites this paper
• Identification of anti-filarial leads against aspartate semialdehyde dehydrogenase of Wolbachia endosymbiont of Brugia malayi: combined molecular docking and molecular dynamics approaches

  2019cites this paper
• Computer-based techniques for lead identification and optimization I: Basics

  2019cites this paper
• An integrated in silico screening strategy for identifying promising disruptors of p53-MDM2 interaction

  2019cites this paper
• Identification of Novel 3-Hydroxy-pyran-4-One Derivatives as Potent HIV-1 Integrase Inhibitors Using in silico Structure-Based Combinatorial Library Design Approach

  2019cites this paper
• Molecular modeling, simulation and principal component analysis of binding of resveratrol and its analogues with DNA

  2019cites this paper
• Structure-activity relationship studies and in vitro and in vivo anticancer activity of novel 3-aroyl-1,4-diarylpyrroles against solid tumors and hematological malignancies.

  2019cites this paper
• An Inhibitor of Fatty Acid Synthase Thioesterase Domain with Improved Cytotoxicity against Breast Cancer Cells and Stability in Plasma

  2019cites this paper
• Molecular Informatics Studies of the Iron-Dependent Regulator (ideR) Reveal Potential Novel Anti-Mycobacterium ulcerans Natural Product-Derived Compounds

  2019influential citation
• The Distribution of Standard Deviations Applied to High Throughput Screening

  2019cites this paper
• Anti-methanogenic effect of rhubarb (Rheum spp.) – An in silico docking studies on methyl-coenzyme M reductase (MCR)

  2019cites this paper
• Synthesis, Antimicrobial Evaluation and Docking Study of Some Pyrazole Bearing [1, 2,4]Triazolo[3, 4‐b][1, 3,4]thiadiazole Derivatives

  2018cites this paper
• Identification of potential drugs targeting L,L‐diaminopimelate aminotransferase of Chlamydia trachomatis: An integrative pharmacoinformatics approach

  2018cites this paper
• Wisdom of crowds for synthetic accessibility evaluation.

  2018cites this paper
• Antitubercular and Molecular Docking Studies of Some 5-Arylmethylene – Pyrimidine -2, 4, 6-Triones

  2018cites this paper
• Computer-Aided Discovery of Small Molecule Inhibitors of Transcriptional Activity of TLX (NR2E1) Nuclear Receptor

  2018cites this paper
• Tight-Binding Inhibition of Human Monoamine Oxidase B by Chromone Analogs: A Kinetic, Crystallographic, and Biological Analysis.

  2018cites this paper
• Computational Assessment of Pharmacokinetics and Biological Effects of Some Anabolic and Androgen Steroids

  2018influential citation