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ZINCPharmer: pharmacophore search of the ZINC database
2012
Nucleic Acids Research
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ZINCPharmer (http://zincpharmer.csb.pitt.edu) is an online interface for searching the purchasable compounds of the ZINC database using the Pharmer pharmacophore search technology. ...
The results can be immediately viewed, or the aligned structures may be downloaded for off-line analysis. ZINCPharmer enables the rapid and interactive search of purchasable chemical space. ...
ACKNOWLEDGEMENTS The ZINC database is incorporated into ZINCPharmer by permission. We thank NIH for supporting this resource. ...
doi:10.1093/nar/gks378
pmid:22553363
pmcid:PMC3394271
fatcat:hui7siifgrdofelktb3g7jop74
A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool
2015
PLoS ONE
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Facilitated by ZincPharmer, an open access online interactive pharmacophore search of the ZINC database, the experience resulted in the development of a novel classification scheme that successfully predicted ...
Pose prediction of compound 6. Receptor structure and binding site residues of 3I65 are shown in blue. Compound 6 is shown in magenta sticks. (a) Compound 6 aligned to the pharmacophore of Fig 1. ...
We would also like to thank the students of the University of Pittsburgh TECBio REU and the UPCI Summer Academy.
Author Contributions ...
doi:10.1371/journal.pone.0134697
pmid:26258606
pmcid:PMC4530941
fatcat:kae35r6vu5avlaaqdspdnawviy
Pharmacophore and ligand-guided screening of antibacterial leads targeting antibiotic resistance factor in Gram-negative bacteria
[article]
2018
arXiv
pre-print
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A total of 8166 hit molecules obtained from ZincPharmer pharmacophore-based screening and PubMed ligand similarity search were further examined through individual two-step semi-flexible docking simulation ...
In this study, a combination of pharmacophore- and ligand-based approach has been employed to explore novel potent EptA inhibitors among millions of commercially-available compounds and approved drugs. ...
and their support towards the publication of this study. ...
arXiv:1803.04661v1
fatcat:fwbblyt7svblhktmaltiadqaoy
DISCOVERY OF NOVEL GLUCOKINASE ACTIVATORS THROUGH STRUCTURE-BASED PHARMACOPHORE MODELING, VIRTUAL SCREENING AND MOLECULAR DOCKING APPROACHES
2021
International Journal of Biology Pharmacy and Allied Sciences
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In this study, structure-based Pharmacophore model was generated; virtual screening was performed using Asinex and Zinc database library compounds. ...
The prevalence of Diabetes mellitus has been increasing day-by-day. Available drug therapies are associated with some side-effects. ...
Virtual Screening of Asinex and
ZincPharmer databases
The generated Pharmacophore model was
then copied to screening perspective of
Ligand Scout software. ...
doi:10.31032/ijbpas/2021/10.10.1048
fatcat:auefvgkwtfgpxeziekfnmd3g74
Repurposing Hydroxychloroquine as a Model Drug for the Prediction of Potential SARS-CoV-2 Inhibitor
2020
European Journal of Engineering Research and Science
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To exhaustively assess the benefit of hydroxychloroquine in the search for SARS-CoV-2 cure, this paper repositioned hydroxychloroquine as a model for virtual screening on the ZINC database. ...
The binding scores of the top five ligands were higher than that of the reference molecule. ...
Pharmacophore-based virtual screening and database preparation The pharmacophoric features of hydroxychloroquine were used as a reference model to search the ZINC database for hit ligands with similar ...
doi:10.24018/ejers.2020.5.9.2056
fatcat:4xbyhjqbgfhk5cbtspws3uhb2y
Pharmacophore and Virtual Screening of JAK3 inhibitors
English
2014
Bioinformation
English
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The statistically significant pharmacophore hypothesis of AAHR.92 with r 2 value of 0.942 was used as 3D query to search against 3D database namely Zincpharmer. ...
In this study, about 116 JAK3 inhibitors were collected from the literature and were used to build four-point pharmacophore model using Phase (Schrodinger module). ...
Methodology: Dataset
Virtual screening Virtual screening was carried out using ZincPharmer (zincpharmer.csb.pitt.edu ) which uses the pharmacophore to efficiently search the ZINC database of fixed conformers ...
doi:10.6026/97320630010157
pmid:24748756
pmcid:PMC3974243
fatcat:7x3mau5i75fjbhqwex4ae4ociq
Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP protein
2021
Scientific Reports
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Overexpression of the protein decreased the apoptosis process in the cell and resulting development of cancer. ...
To identify natural compound, a structure-based pharmacophore model to the protein active site cavity was generated following by virtual screening, molecular docking and molecular dynamics (MD) simulation ...
Acknowledgements This project was funded by the National Plan for Science, Technology and Innovation (MAARIFAH) -King Abdulaziz City for Science and Technology -the Kingdom of Saudi Arabia -award number ...
doi:10.1038/s41598-021-83626-x
pmid:33603068
pmcid:PMC7892887
fatcat:5bf4yfdntnfmdnn6i4mon2b32a
PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure
2012
Nucleic Acids Research
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PocketQuery rapidly focuses attention on the key interacting residues of an interaction using a 'druggability' score that provides an estimate of how likely the chemical mimicry of a cluster of interface ...
PocketQuery (http://pocketquery.csb.pitt.edu) is a web interface for exploring the properties of protein-protein interaction (PPI) interfaces with a focus on the discovery of promising starting points ...
ZINCPharmer is a general interactive pharmacophore search technology for the ZINC database (34) . ZINCPharmer is routinely updated to search the most recent set of purchasable compounds from ZINC. ...
doi:10.1093/nar/gks336
pmid:22523085
pmcid:PMC3394328
fatcat:xgatl54cavahxor2k6avjzceau
An Integrated Computational Approach for Plant-Based Protein Tyrosine Phosphatase Non-Receptor Type 1 Inhibitors
2017
Current Computer - Aided Drug Design
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A common feature pharmacophore model was generated. Pharmacophore-based screening of plant-derived compounds of the ZINC database was conducted using ZINCpharmer. ...
The present study proposes a pipeline for the development of effective and plant-derived anti-diabetic drugs that may be safer and better tolerated. ...
Both authors had a significant role in the conceptualization and writing of this manuscript. ...
doi:10.2174/1573409913666170406145607
pmid:28382867
pmcid:PMC5744427
fatcat:zinxeyf6sbdg3c3kbltyfcmdu4
Ligand-Based Pharmacophore Modeling, Molecular Docking, and Molecular Dynamic Studies of Dual Tyrosine Kinase Inhibitor of EGFR and VEGFR2
2020
International Journal of Molecular Sciences
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Firstly, the ligand-based pharmacophore model for each target was setup to screen of ZINC database of purchasable compounds. ...
The hit compounds obtained by pharmacophore screening were then further screened by molecular docking studies. ...
The previously obtained pharmacophore model of EGFR was submitted to ZINCPharmer, to search hits from the ZINC database of "purchasable compounds" consist of 22,723,923 compounds [32] . ...
doi:10.3390/ijms21207779
pmid:33096664
fatcat:nsdpiron5vcghecrvrogtovnxm
Identification of novel inhibitors for TNFα, TNFR1 and TNFα-TNFR1 complex using pharmacophore-based approaches
2019
Journal of Translational Medicine
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TNFα-TNF receptor-1 (TNFR1) signaling contributes to the pathological processes of these disorders. ...
The current study is focused on finding novel small molecules that can directly bind to TNFα and/or TNFR1, preventing the interaction between TNFα or TNFR1, and regulating downstream signaling pathways ...
Acknowledgements The authors would like to acknowledge Dr. Anton Lennikov (University of Missouri, Columbia, Missouri, USA) for his insightful discussion, and Ms. ...
doi:10.1186/s12967-019-1965-5
pmid:31266509
pmcid:PMC6604280
fatcat:a5asttnmxng7dfmsxwf4gxigea
Finding inhibitors for PCSK9 using computational methods
2021
PLoS ONE
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Selected models were later screened against the ZINC database using ZINCPHARMER to define potential drug candidates that were docked with the target protein to understand their interactions. ...
To start with, reported ACE inhibitors were incorporated into pharmacophore designing using PharmaGist to produce pharmacophore models. ...
Acknowledgments The authors would like to thank the editor and the anonymous reviewers, whose comments helped improve the quality of the final manuscript. ...
doi:10.1371/journal.pone.0255523
pmid:34351937
pmcid:PMC8341581
fatcat:ppgabimibrca7njlbuokclxacq
Virtual Screening and Statistical Analysis in the Design of New Caffeine Analogues Molecules with Potential Epithelial Anticancer Activity
2018
Current pharmaceutical design
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The generated pharmacophore was used to select 350 molecules available at the ZINCpharmer server, followed by reduction to 24 molecules, after selection using the Tanimoto index, yielding 10 molecules ...
For this, a training set of 21 molecules was used for pharmacophore perception procedures. ...
ACKNOWLEDGEMENTS We acknowledge the support provided by the PROPESP/UFPA. ...
doi:10.2174/1381612823666170711112510
pmid:28699538
pmcid:PMC5944109
fatcat:zsmj3evwxzeotjzglugwsiwcu4
Pharmacophore feature-based virtual screening for finding potent GSK-3 inhibitors using molecular docking and dynamics simulations
2016
Bioinformation
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In the present study, we performed pharmacophore feature-based virtual screening for identifying potent targetspecific GSK-3 inhibitors. ...
These findings are expected to play a crucial role in the binding of target-specific GSK-3 inhibitors. ...
Chauhan gratefully acknowledges the Head, Department of Pharmaceutical Chemistry, Saraswati Institute of Pharmaceutical Sciences, Gandhinagar, India, for providing necessary facilities required to execute ...
doi:10.6026/97320630012391
pmid:28293069
pmcid:PMC5320924
fatcat:nlrzocasyfeq7gi6gcgycxfjae
Identification and Validation of a Potent Dual Inhibitor of the P. falciparum M1 and M17 Aminopeptidases Using Virtual Screening
2015
PLoS ONE
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Starting from the ZINC database of purchasable compounds, sequential 3D-pharmacophore and molecular docking steps were applied to filter the virtual 'hits'. ...
To this end, we undertook a virtual screen of the ZINC database of purchasable subsets (~18 millions of compounds) [17, 18] and used successive 3D-pharmacophore and molecular docking to filter the virtual ...
Acknowledgments We thank the Australian Synchrotron for beam time (MXCAP 8208) and technical assistance.
Author Contributions ...
doi:10.1371/journal.pone.0138957
pmid:26406322
pmcid:PMC4583420
fatcat:5m4khtw3jrd3rodj4vpnmt3aai
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