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MTiOpenScreen: a web server for structure-based virtual screening
2015
Nucleic Acids Research
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In this line, we developed the new web server MTiOpenScreen dedicated to small molecule docking and virtual screening. ...
The MTiOpenScreen web server is free and open to all users at http://bioserv.rpbs. univ-paris-diderot.fr/services/MTiOpenScreen/. ...
Here we present the new web server MTiOpenScreen dedicated to small molecule docking and virtual screening. ...
doi:10.1093/nar/gkv306
pmid:25855812
pmcid:PMC4489289
fatcat:rt6ebhk2gbfbbhnvmmalg4iybm
A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments
2019
International Journal of Molecular Sciences
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Here, we describe a free web-based protocol dedicated to small-molecule virtual screening that includes three major steps: ADME-Tox filtering (via the web service FAF-Drugs4), docking-based virtual screening ...
(via the web service MTiOpenScreen), and molecular mechanics optimization (via the web service AMMOS2 [Automatic Molecular Mechanics Optimization for in silico Screening]). ...
: ADME-Tox filtering via the web server FAF-Drugs4 [19] (http://fafdrugs4.mti.univ-parisdiderot.fr), docking-based virtual screening via the web server MTiOpenScreen [20] (http://bioserv.rpbs.univ-paris-diderot.fr ...
doi:10.3390/ijms20184648
pmid:31546814
pmcid:PMC6769597
fatcat:az52xjmesvc6tgsx4un2vzmhiu
Virtual screening on the web for drug repurposing: a primer
2021
Journal of Biological Methods
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We describe a procedure of performing in silico (virtual) screening using a web-based service, the MTiOpenScreen, whichis freely accessible to non-commercial users. ...
The results can be readily examined graphically on the web site or downloaded for studying in a local molecular graphics program such as PyMOL. ...
The purpose of this article is to outline a protocol of performing virtual screening (VS) using web services and tools which are free for non-profit users. ...
doi:10.14440/jbm.2021.351
pmid:34104664
pmcid:PMC8175336
fatcat:h4jgklb6zjgunixjbjaj6qzll4
Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets
2018
OncoTarget
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structure-based virtual screening studies. ...
The three compounds libraries are implemented in the MTiOpenScreen web server that allows users to perform structure-based virtual screening computations on their selected protein targets. ...
ACKNOWLEDGMENTS We thank the Inserm Institute and the University Paris Diderot for continuous supports.
CONFLICTS OF INTEREST The authors declare no conflicts of interest. ...
doi:10.18632/oncotarget.25966
pmid:30190791
pmcid:PMC6122352
fatcat:l76txsj4f5ghtmihxgu7upau7q
ACFIS: a web server for fragment-based drug discovery
2016
Nucleic Acids Research
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This makes the AC-FIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/. ...
However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). ...
We presented ACFIS, a computer-aided FBDD web server, to provide solutions for fragment virtual screening and to assist scientists in the new hits identification. ...
doi:10.1093/nar/gkw393
pmid:27150808
pmcid:PMC4987934
fatcat:4a3xxy5wkrgktdyddfhe6633ja
Homology Modeling, Docking, Absorption, Distribution, Metabolism, Excretion and Toxicity Studies and Prediction of Deleterious Non-Synonymous Single Nucleotide Polymorphisms (Nssnps) of Thiamin Phosphate Synthase: A Potential Drug Target in Plasmodium Falciparum
2020
Indian Journal of Pharmaceutical Sciences
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The 3D structure was constructed using SWISS-MODEL and several computer-aided approaches were used for screening of drug-like compounds. ...
Out of 156 compounds screened, only those 98 compounds which followed the Lipinski's rule of five were used for molecular docking. ...
Acknowledgments: Authors thankful to Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, India, for providing required facilities to carry out this research work. ...
doi:10.36468/pharmaceutical-sciences.692
fatcat:zydbmcenpvbibhjsp2l5mbpgha
Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace
2020
Briefings in Bioinformatics
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Today, user-friendly web-based tools are available to help scientists perform virtual screening experiments. ...
This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule ...
We then discuss ligand-based virtual screening (LBVS) and structure-based virtual screening (SBVS) tools. ...
doi:10.1093/bib/bbaa034
pmid:32187356
pmcid:PMC7986591
fatcat:mq3csvzjkfekhpjfti2wmyipxi
Structure-based drug repositioning over the human TMPRSS2 protease domain: search for chemical probes able to repress SARS-CoV-2 Spike protein cleavages
2020
European Journal of Pharmaceutical Sciences
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To block the catalytic site or the exosite of TMPRSS2 we used structure-based virtual screening computations and two different collections of approved, investigational and experimental drugs. ...
There is no experimental structure for TMPRSS2 but it is possible to develop quality structural models for the serine protease domain using comparative modeling strategies as such domains are highly structurally ...
The MTiOpenScreen web-server with the Drugs-lib collection N. Singh, et al. ...
doi:10.1016/j.ejps.2020.105495
pmid:32730844
pmcid:PMC7384984
fatcat:aeqv3xig3nhudfztbqs7hlra6m
Identification of Potential Inhibitors of Zika Virus NS5 RNA-Dependent RNA Polymerase Through Virtual Screening and Molecular Dynamic Simulations
2020
Saudi Pharmaceutical Journal
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The non-structural proteins of flaviviruses are suitable active targets for inhibitory drugs due to their role in pathogenicity. ...
Here we have performed virtual screening to identify suitable ligands that can potentially halt the ZIKV NS5 RNA dependent RNA polymerase (RdRp). ...
Acknowledgements The authors also extend their appreciation to the Deanship of Scientific research at King Saud University for funding this work through research group no.(RG-1440-009).
Appendix A. ...
doi:10.1016/j.jsps.2020.10.005
pmid:33424251
pmcid:PMC7783101
fatcat:nglvkij33ncnde6ol4u3kbbtyi
Cloud-Based High Throughput Virtual Screening in Novel Drug Discovery
[chapter]
2019
Msphere
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This may be a seed for further inter-disciplinary development of VS to be applied by drug hunters. ...
Chemical datasets can be built, libraries can be analyzed, and structure-based or ligand-based VS studies can be performed with cloud technologies. ...
for structure-based VS service as a web service HDOCK [108] X hdock.phys.hust.edu.cn Protein-protein and proteinnucleic acid docking server HADDOCK Web Server [109] X milou.science.uu.nl/ services/HADDOCK2.2 ...
doi:10.1007/978-3-030-16272-6_9
fatcat:dihdpicowrg4vbsirumu3o4ezi
Pharmit: interactive exploration of chemical space
2016
Nucleic Acids Research
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Users can import, create and edit virtual screening queries in an interactive browser-based interface. ...
Pharmit (http://pharmit.csb.pitt.edu) provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape and energy minimization. ...
ACKNOWLEDGEMENTS We thank Charles Yuan for assistance with web site design and the many early users of Pharmit for their helpful feedback. ...
doi:10.1093/nar/gkw287
pmid:27095195
pmcid:PMC4987880
fatcat:3pl24dadqnfnppuxan7dg2vgja
Identification of Potential HCV Inhibitors Based on the Interaction of Epigallocatechin-3-Gallate with Viral Envelope Proteins
2021
Molecules
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The potential lead molecules were predicted using ligand-based as well as structure-based virtual screening methods. The compounds obtained were then screened through PyRx. ...
The in silico approach in the drug discovery process is an efficient method in identifying inhibitors for various diseases. ...
Structure-Based Virtual Screening Dockblaster [33] , pep mms mimic [34] , and MTiOpenScreen [35] were used for drug mining against the E2 protein of HCV to find its potential inhibitors. ...
doi:10.3390/molecules26051257
pmid:33652639
pmcid:PMC7956288
fatcat:2pl37yuturh5bapfdqyt7w7eqy
Autonomous molecule generation using reinforcement learning and docking to develop potential novel inhibitors
2020
Scientific Reports
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The free web server is available at http://morld.kaist.ac.kr . ...
We also demonstrated MORLD's ability to generate predicted novel agonists for the D4 dopamine receptor (D4DR) from scratch without virtual screening on an ultra large compound library. ...
W.J. performed the computations and developed a web server. D.K. supervised the findings of this work. W.J. and D.K. wrote the final manuscript. ...
doi:10.1038/s41598-020-78537-2
pmid:33328504
fatcat:3egt5e4rmvepzjexuaypxrki4q
Molecular docking analysis of pyruvate kinase M2 with a potential inhibitor from the ZINC database
2021
Bioinformation
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Thus, we document the optimal molecular docking features of a compound having ID ZINC000034285235 with PKM2 for further consideration. ...
based virtual screening. ...
Docking was carried out on the MTiOpenScreen server with AutoDock Vina and with AutoDock on MTiAutoDock server [21] . ...
doi:10.6026/97320630017139
fatcat:lzlljuhdqjgezei52my2wzlj5q
Molecular Docking: Shifting Paradigms in Drug Discovery
2019
International Journal of Molecular Sciences
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Molecular docking is an established in silico structure-based method widely used in drug discovery. ...
knowing a priori the chemical structure of other target modulators. ...
Similarly, the ACTP [123] web server enables the screening of a ligand by using the Libdock docking protocol [154] . ...
doi:10.3390/ijms20184331
pmid:31487867
pmcid:PMC6769923
fatcat:pxh6aqni2vehxk7kyjwujciwf4
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