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MTiOpenScreen: a web server for structure-based virtual screening

Céline M. Labbé, Julien Rey, David Lagorce, Marek Vavruša, Jérome Becot, Olivier Sperandio, Bruno O. Villoutreix, Pierre Tufféry, Maria A. Miteva
2015 Nucleic Acids Research  
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

Nathalie Lagarde, Elodie Goldwaser, Tania Pencheva, Dessislava Jereva, Ilza Pajeva, Julien Rey, Pierre Tuffery, Bruno O. Villoutreix, Maria A. Miteva
2019 International Journal of Molecular Sciences  
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

Yu Wai Chen, Chin-Pang Bennu Yiu, Kwok-Yin Wong
2021 Journal of Biological Methods  
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

Nathalie Lagarde, Julien Rey, Aram Gyulkhandanyan, Pierre Tufféry, Maria A. Miteva, Bruno O. Villoutreix
2018 OncoTarget  
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

Ge-Fei Hao, Wen Jiang, Yuan-Nong Ye, Feng-Xu Wu, Xiao-Lei Zhu, Feng-Biao Guo, Guang-Fu Yang
2016 Nucleic Acids Research  
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

S. K. SINGH, M.S. REDDY
2020 Indian Journal of Pharmaceutical Sciences  
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  
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

Natesh Singh, Etienne Decroly, Abdel-Majid Khatib, Bruno O. Villoutreix
2020 European Journal of Pharmaceutical Sciences  
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

Noreen, Roshan Ali, Syed Lal Badshah, Muhammad Faheem, Sumra Wajid Abbasi, Riaz Ullah, Ahmed Bari, Syed Babar Jamal, Hafiz Majid Mahmood, Adnan Haider, Sajjad Haider
2020 Saudi Pharmaceutical Journal  
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]

Abdurrahman Olğaç, Aslı Türe, Simla Olğaç, Steffen Möller
2019 Msphere  
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

Jocelyn Sunseri, David Ryan Koes
2016 Nucleic Acids Research  
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

Fareena Shahid, Noreen, Roshan Ali, Syed Lal Badshah, Syed Babar Jamal, Riaz Ullah, Ahmed Bari, Hafiz Majid Mahmood, Muhammad Sohaib, Siddique Akber Ansari
2021 Molecules  
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

Woosung Jeon, Dongsup Kim
2020 Scientific Reports  
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

Pankaj Sharma, Department of Biotechnology, UIET, Maharshi Dayanand University Rohtak Haryana
2021 Bioinformation  
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

Luca Pinzi, Giulio Rastelli
2019 International Journal of Molecular Sciences  
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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