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FAF-Drugs: free ADME/tox filtering of compound collections

M. A. Miteva, S. Violas, M. Montes, D. Gomez, P. Tuffery, B. O. Villoutreix
2006 Nucleic Acids Research  
FAF-Drugs is an online service based on Frowns (a chemoinformatics toolkit) that allows users to process their own compound collections via simple ADME/Tox filtering rules such as molecular weight, polar  ...  Other utilities and several compound collections suitable for in silico screening are available at our site. FAF-Drugs can be accessed at  ...  The authors would like to thank OpenEye Scientific Software (CA, USA, http://www.eyesopen.com) for providing Omega and Filter and for allowing us to process several compound collections.  ... 
doi:10.1093/nar/gkl065 pmid:16845110 pmcid:PMC1538885 fatcat:5ba64iamq5e3jp5hb7odggipui

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

David Lagorce, Olivier Sperandio, Hervé Galons, Maria A Miteva, Bruno O Villoutreix
2008 BMC Bioinformatics  
Results: This paper presents FAF-Drugs2, a free adaptable tool for ADMET filtering of electronic compound collections.  ...  In addition to filtered collections, FAF-Drugs2 can provide, via Gnuplot, several distribution diagrams of major physicochemical properties of the screened compound libraries.  ...  In this article, we describe a new enhanced version of FAF-Drugs, which was originally based on the free chemoinformatics toolkit Frowns [10] .  ... 
doi:10.1186/1471-2105-9-396 pmid:18816385 pmcid:PMC2561050 fatcat:csglhyqjqfcxnmgyo5rjfvktau

Frog: a FRee Online druG 3D conformation generator

T. B. Leite, D. Gomes, M.A. Miteva, J. Chomilier, B.O. Villoutreix, P. Tuffery
2007 Nucleic Acids Research  
free 1D/2D to 3D structure generators.  ...  To achieve such process, the 3D structures of the small chemical compounds have to be generated.  ...  Usually, libraries have to be filtered (ADME/tox filtering) to remove compounds with unacceptable physico-chemical properties and disease-causing chemical functionalities.  ... 
doi:10.1093/nar/gkm289 pmid:17485475 pmcid:PMC1933180 fatcat:afdrv26v3rf5pnnftn7pz6igsi

Chemoinformatics-based enumeration of chemical libraries: a tutorial

Fernanda I. Saldívar-González, C. Sebastian Huerta-García, José L. Medina-Franco
2020 Journal of Cheminformatics  
isoindolinone based compounds as potential acetylcholinesterase inhibitors.  ...  Virtual compound libraries are increasingly being used in computer-assisted drug discovery applications and have led to numerous successful cases.  ...  The relative size of the data set is represented by the size of the data point. d ADME/Tox profile of the three databases calculated with the free server FAF-Drugs.  ... 
doi:10.1186/s13321-020-00466-z pmid:33372622 fatcat:5j76a5cf3rgnxlwoduvhdgopbm

In Silico-In Vitro Screening of Protein-Protein Interactions: Towards the Next Generation of Therapeutics

Bruno Villoutreix, Karine Bastard, Olivier Sperandio, Robin Fahraeus, Jean-Luc Poyet, Fabien Calvo, Benoit Deprez, Maria Miteva
2008 Current Pharmaceutical Biotechnology  
URLs for several recent free packages or servers are also provided.  ...  of therapeutics.  ...  FAF-Drugs: Free collections in 3D (and ADME/tox) and utilities [206] http://zinc.docking.org ZINC: Free collections in 3D (and ADME/tox) [208] http://bioweb.ucr.edu/ChemMine ChemMine: Free collections  ... 
doi:10.2174/138920108783955218 pmid:18393867 fatcat:db63x2enijagzdo34ttc4hqshy

MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening

Nicolas Sauton, David Lagorce, Bruno O Villoutreix, Maria A Miteva
2008 BMC Bioinformatics  
The number of protein targets with a known or predicted tri-dimensional structure and of drug-like chemical compounds is growing rapidly and so is the need for new therapeutic compounds or chemical probes  ...  Conclusion: MS-DOCK can be easily used for the generation of multi-conformer libraries and for shape-based filtering within a multi-step structure-based screening protocol in order to shorten computation  ...  The physico-chemical properties of both validation compounds sets were assessed via the ADME/ tox filtering tool FAF-Drugs [55, 56] available on the RPBS web server [54] .  ... 
doi:10.1186/1471-2105-9-184 pmid:18402678 pmcid:PMC2373571 fatcat:lbpwtep3rffwxcc67bey3vy5bu

Development of a Novel Virtual Screening Cascade Protocol to Identify Potential Trypanothione Reductase Inhibitors

Rolando Perez-Pineiro, Asdrubal Burgos, Deuan C. Jones, Lena C. Andrew, Hortensia Rodriguez, Margarita Suarez, Alan H. Fairlamb, David S. Wishart
2009 Journal of Medicinal Chemistry  
Assays measuring the inhibiting effect of these compounds on T. cruzi and T. brucei TryR confirm their potential for further rational optimization.  ...  Compounds were ranked by an exhaustive conformational consensus scoring approach that employs a rank-by-rank strategy by combining both scoring functions.  ...  This material is available free of charge via the Internet at http://pubs.acs.org.  ... 
doi:10.1021/jm801306g pmid:19296695 pmcid:PMC2659691 fatcat:ogyfolznxnaivlyr573gff34iy

Comparative analysis of PknB inhibitors for reactivity and toxicity [article]

Nathan Wlodarchak, Jeff Beczkiewicz, Steven Seitz, Zhengqing Ye, John Feltenberger, J Muse Davis, Rob Striker
2018 bioRxiv   pre-print
These inhibitors typically are derived from screens of known kinase inhibitors and most share similar chemical properties as their parent compounds were all designed for optimal pharmacokinetic properties  ...  We found that the compound is highly reactive with thiolating agents and has appreciable toxicity in a zebrafish animal model.  ...  The compound sdf file was submitted to the FAF-Drugs4 (Free ADME-Tox Filtering Tool) [4] server for analysis with default parameters. R406 was similarly built and analyzed as a control.  ... 
doi:10.1101/423061 fatcat:if4qghudabcwhcnr7fmb4go2gm

Drug-Like ProteinProtein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

Bruno O. Villoutreix, Melaine A. Kuenemann, Jean-Luc Poyet, Heriberto Bruzzoni-Giovanelli, Céline Labbé, David Lagorce, Olivier Sperandio, Maria A. Miteva
2014 Molecular Informatics  
about the modulation of PPIs with small drug-like molecules. In fact, several success stories were reported both, at the preclinical and clinical stages.  ...  We first introduce the field of proteinÀprotein interaction research, discuss key challenges and comment recently reported in silico packages, protocols and databases dedicated to PPIs.  ...  Rognan for the organization of the 2014 International Workshops in Chemoinformatics.  ... 
doi:10.1002/minf.201400040 pmid:25254076 pmcid:PMC4160817 fatcat:kryzjqycvrg5vd3surg4sdxrgy

Computational and Experimental Advances in Drug Repositioning for Accelerated Therapeutic Stratification

Khader Shameer, Ben Readhead, Joel T. Dudley
2015 Current Topics in Medicinal Chemistry  
Efficient tools are now available for systematic drug-repositioning methods using large repositories of compounds with biological activities.  ...  An increasing collection of available computational and experimental methods that leverage molecular and clinical data enable diverse drug repositioning strategies.  ...  13,000 metabolites, 16,000 drugs and 2200 toxic compounds Free ADME/tox Filtering (FAF-Drugs) Webserver for screening of small molecule li- brary for absorption, distribution, metabolism, excretion  ... 
doi:10.2174/1568026615666150112103510 pmid:25579574 fatcat:uryq36httvcwrfub36lstr6tw4

e-LEA3D: a computational-aided drug design web server

D. Douguet
2010 Nucleic Acids Research  
The second tool offers a traditional virtual screening and filtering of an uploaded library of compounds.  ...  The de novo approach is an alternative to a blind virtual screening of large compound collections.  ...  The authors also thank the developers of free and/or open source software: Frog, Jmol, Chemis3D, mol2ps, ACDLABS for the structure drawing applet and OpenBabel.  ... 
doi:10.1093/nar/gkq322 pmid:20444867 pmcid:PMC2896156 fatcat:4nwr32n5lngvhjy2pt4uzna2pa

In silico Prediction, Characterization, Molecular Docking, and Dynamic Studies on Fungal SDRs as Novel Targets for Searching Potential Fungicides Against Fusarium Wilt in Tomato

Mohd Aamir, Vinay Kumar Singh, Manish Kumar Dubey, Mukesh Meena, Sarvesh Pratap Kashyap, Sudheer Kumar Katari, Ram Sanmukh Upadhyay, Amineni Umamaheswari, Surendra Singh
2018 Frontiers in Pharmacology  
The docked complexes were further refined and rescored from their docked poses through 50 ns long MD simulations, and binding free energies (ΔGbind) calculations, using MM/GBSA analysis, revealed Oxathiapiprolin  ...  Vascular wilt of tomato caused by Fusarium oxysporum f.sp. lycopersici (FOL) is one of the most devastating diseases, that delimits the tomato production worldwide.  ...  The FAF-drugs 4.0 tool performed the computational prediction of some ADME-Tox properties (adsorption, distribution, metabolism, excretion, and toxicity) for Famoxadone and it was found that the drug is  ... 
doi:10.3389/fphar.2018.01038 pmid:30405403 pmcid:PMC6204350 fatcat:xmon6xvabra2nidkn347unqgh4