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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  
Frog is an on-line service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions.  ...  Tests show that Frog is able to generate bioactive conformations close to those observed in crystallographic complexes. Frog can be accessed at http://bioserv.rpbs.jussieu.fr/ Frog.html.  ...  Very few free on-line tools are available to generate the 3D conformation of compounds.  ... 
doi:10.1093/nar/gkm289 pmid:17485475 pmcid:PMC1933180 fatcat:afdrv26v3rf5pnnftn7pz6igsi

Frog2: Efficient 3D conformation ensemble generator for small compounds

M. A. Miteva, F. Guyon, P. Tuffery
2010 Nucleic Acids Research  
Frog is a web tool dedicated to small compound 3D generation.  ...  Here we present the new version, Frog2, which allows the generation of conformation ensembles of small molecules starting from either 1D, 2D or 3D description of the compounds.  ...  Yet, very few free tools are available for a single or multiple conformation generation.  ... 
doi:10.1093/nar/gkq325 pmid:20444874 pmcid:PMC2896087 fatcat:zk3t3umazjepbleihtpqe76prq

DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

David Lagorce, Tania Pencheva, Bruno O Villoutreix, Maria A Miteva
2009 BMC Chemical Biology  
The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine.  ...  A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out.  ...  Recently the web-service Frog (a mixed rule-based data-based approach) [25] has been proposed and aims at providing on-line generation of a single or ensembles of 3D conformation for drug-like compounds  ... 
doi:10.1186/1472-6769-9-6 pmid:19912625 pmcid:PMC2781789 fatcat:26k6tsknz5atlp55dan6zrpyhu

wwLigCSRre: a 3D ligand-based server for hit identification and optimization

O. Sperandio, M. Petitjean, P. Tuffery
2009 Nucleic Acids Research  
The wwLigCSRre web server performs ligand-based screening using a 3D molecular similarity engine.  ...  Its aim is to provide an online versatile facility to assist the exploration of the chemical similarity of families of compounds, or to propose some scaffold hopping from a query compound.  ...  All the subsets were generated in 3D with Frog (31) and a maximum of 50 best scored conformations per molecule was generated using the tool MS-Dock (32).  ... 
doi:10.1093/nar/gkp324 pmid:19429687 pmcid:PMC2703967 fatcat:wig5sa3wnne3nka5v246ob7njy

Dipeptidyl Peptidase IV Inhibitory Activity of Berberine and Mangiferin: An In Silico Approach

Ipseeta Ray Mohanty
2015 International Journal of Clinical Endocrinology and Metabolism  
All these structures were retrieved in SDF fi le format which was further converted into 3D format using Frog v2.14 (FRee On line druG conformation generation) [17] .  ...  In the Frog online server, the input was maintained as '1D to 2D' and the input drug description was 'SDF' fi le. In the calculation parameters the output format was maintained as 'PDB'.  ... 
doi:10.17352/ijcem.000024 fatcat:jdb6bxmqjzes3k6ktazf6ruinu

Homology Modelling and Molecular Docking Studies of Selected Substituted Benzo[d]imidazol-1-yl)methyl)benzimidamide Scaffolds on Plasmodium falciparum Adenylosuccinate Lyase Receptor

Gbolahan O Oduselu, Olayinka O Ajani, Yvonne U Ajamma, Benedikt Brors, Ezekiel Adebiyi
2019 Bioinformatics and Biology Insights  
PfADSL 3D structure was modelled using SWISS-MODEL, whereas the compounds were designed using ChemDraw Professional.  ...  Thus, they could be further synthesised and developed into active commercial antimalarial drugs.  ...  Also, ChemDraw was used to generate the simplified molecular-input line-entry system (SMILES) that were converted to their corresponding 3D structures using FRee Online druG 3D conformation generator (  ... 
doi:10.1177/1177932219865533 pmid:31391779 pmcid:PMC6669854 fatcat:xl44e54rlvflbgonwvwjkfirui

Virtual Ligand Screening for Structure-based Drug Design: Approaches and Progress

Olivier Sperandio, Maria A. Miteva, Bruno O. Villoutreix
2007 Bioautomation  
Today technologies like combinatorial chemistry and high-throughput screening (HTS) authorize biological assays of a large number of small molecules against the therapeutically relevant targets.  ...  Recent progress in human genomics and proteomics has significantly increased the number of macromolecular targets potentially involved in drug discovery campaigns.  ...  Recently FROG, a tool to generate multiple 3D conformations of compounds has been reported [61] (http://bioserv.rpbs.jussieu.fr/Frog.html).  ... 
doaj:ff15b8741a9e4e538ca40e68434b1c85 fatcat:ky74ryvp6razpkhwimn76hy44q

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  
Key words: virtual ligand screening, structure-based drug design, docking, scoring, drug discovery, protein-protein interaction.  ...  URLs for several recent free packages or servers are also provided.  ...  to 3D conversion none http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ Possible 2D to 3D [317] http://bioserv.rpbs.jussieu.fr/Frog.html Frog: a FRee Online druG 3D conformation generator [318] http:/  ... 
doi:10.2174/138920108783955218 pmid:18393867 fatcat:db63x2enijagzdo34ttc4hqshy

Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics

See Hong Chiu, Lei Xie
2016 Journal of Chemical Information and Modeling  
It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/024513 doi: bioRxiv preprint first posted online Aug. 12, 2015; Significance Drug efficacy  ...  One of the unaddressed challenges in drug discovery is that drug potency determined in vitro is not a reliable indicator of drug activity in humans.  ...  Second, the ligand SMILES string was converted into a 3D molecular ligand structure using Frog [43] as shown in Figure S8 .  ... 
doi:10.1021/acs.jcim.5b00632 pmid:27159844 pmcid:PMC5537004 fatcat:evawxfnokbfezoswhsf54ozxwi

Toward high-throughput predictive modeling of protein binding/unbinding kinetics [article]

See Hong Chiu, Lei Xie
2015 bioRxiv   pre-print
One of the unaddressed challenges in drug discovery is that drug potency determined in vitro is not a reliable indicator of drug efficacy and toxicity in humans.  ...  We find that the coherent coupling of conformational dynamics between protein and ligand may play a critical role in determining the kinetic rate constants of PLI.  ...  Second, the ligand SMILES string was converted into a 3D molecular ligand structure using Frog [43] as shown in Figure S8 .  ... 
doi:10.1101/024513 fatcat:jhnxk4v3rfhrbmjx7phwpjikmi

Could Dermaseptin Analogue be a Competitive Inhibitor for ACE2 Towards Binding with Viral Spike Protein Causing COVID19?: Computational Investigation

P. Chandra Sekar, R. Rajasekaran
2021 International Journal of Peptide Research and Therapeutics  
Markedly, the strong interactions consistently maintained by S1-S4 (K4) complex revealed their conformational transition over the harmonic motion period.  ...  The present study examined the competitive inhibitor activity of a broad spectrum antimicrobial peptide, Dermaseptin-S4 (S4) and its analogues.  ...  The same nonparametric test was performed for all the parameters viz., RMSD, RMSF, Rg, conformational free energies and membrane-free energies of peptides.  ... 
doi:10.1007/s10989-020-10149-w pmid:33488318 pmcid:PMC7811342 fatcat:3k6vckyllzbmpmfwmm4idhdfbe

Current Strategies in Assessment of Nanotoxicity: Alternatives to In Vivo Animal Testing

Hung-Jin Huang, Yu-Hsuan Lee, Yung-Ho Hsu, Chia-Te Liao, Yuh-Feng Lin, Hui-Wen Chiu
2021 International Journal of Molecular Sciences  
In the first step of a docking study, all possible conformations and orientations of each ligand are generated according to the shape of the defined binding site in the protein structure.  ...  Generally, the accuracy and speed of the docking conformation is strongly related to the types of search algorithms used.  ... 
doi:10.3390/ijms22084216 pmid:33921715 fatcat:a6qgvjggnraz7btywkfot3hgdu

Discorhabdin N, a South African Natural Compound, for Hsp72 and Hsc70 Allosteric Modulation: Combined Study of Molecular Modeling and Dynamic Residue Network Analysis

Arnold Amusengeri, Özlem Tastan Bishop
2019 Molecules  
A comparative modeling approach was used to obtain nearly full-length 3D structures of the closed conformation of Hsp72 and Hsc70 proteins.  ...  While drug development has extensively focused on Hsp90 as a potential anticancer target, much less effort has been put against Hsp72.  ...  Conflicts of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationship that could be construed as a potential conflict of interest.  ... 
doi:10.3390/molecules24010188 fatcat:wsrshljahret7psakwxozsjg6e

A molecular journey to check the conformational dynamics of tau tubulin kinase 2 mutations associated with Alzheimer's disease

Shahzaib Ahamad, Hema Kanipakam, Vijay Kumar, Dinesh Gupta
2021 RSC Advances  
The reliable template for TTBK2 was obtained from PDB (6U0K) to generate homology models. 13 he 3D structure was built through I-TASSER online tool using the template selected in the previous step. 24  ...  novel drugs.  ... 
doi:10.1039/d0ra07659g pmid:35424125 pmcid:PMC8693565 fatcat:qjyjnr6knja63gdibh7taisl5m

Seeking the exclusive binding region of phenylalkylamine derivatives on human T‐type calcium channels via homology modeling and molecular dynamics simulation approach

You Lu, Ming Li, Gi Young Lee, Na Zhao, Zhong Chen, Andrea Edwards, Kun Zhang
2021 Pharmacology Research & Perspectives  
Moreover, free-energy perturbation analysis suggests single mutation of lysine at P-loop domain III, or threonine at the P-loop domain II largely reduced the total amount of hydration-free energy in the  ...  Only a few PAAs have the binding specificity on calcium channels, for example, NNC 55-0396.  ...  We used Open Babel 24 to convert the compound format and Frog 25 to find the coordinate of compound conformers in 3D space.  ... 
doi:10.1002/prp2.783 pmid:33984189 pmcid:PMC8118199 fatcat:b4l7vzziircjrmp54zrg5t3mye
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