Rigid-body XP docking with Glide Version 1
This SOP describes the docking of pteridine libraries into PTR1 or DHFR target receptors, using Glide in Schrödinger Maestro with the XP (eXtra Precision) protocol.
SEEK ID: https://fairdomhub.org/sops/447?version=1
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sop_glide-xp-docking.pdf
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Created: 22nd Sep 2020 at 13:21
Last updated: 30th Sep 2020 at 10:03
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Version 1 (earliest) Created 22nd Sep 2020 at 13:21 by Ina Poehner
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Projects: Kinetics on the move - Workshop 2016, COVID-19 Disease Map, NMTrypI - New Medicines for Trypanosomatidic Infections, CoVIDD - Coronavirus interactions in drug discovery - optimization and implementation
Institutions: Kinetics on the move Workshop at HITS, Heidelberg Institute for Theoretical Studies (HITS gGmbH), University of Eastern Finland (UEF)
https://orcid.org/0000-0002-2801-8902
Group Leader, Molecular and Cellular Modeling Group, EML Research, Heidelberg
Projects: NMTrypI - New Medicines for Trypanosomatidic Infections
Web page: https://cordis.europa.eu/programme/id/FP7_HEALTH.2013.2.3.4-2
The New Medicines for Trypanosomatidic Infections - NMTrypI project aimed at obtaining new candidate drugs against Trypanosomatidic infections with appropriate efficiency from the lead phase to the final preclinical phase that are more accessible to patients.
Programme: Drug development for neglected parasitic diseases
Public web page: https://fp7-nmtrypi.eu/
Start date: 1st Feb 2014
End date: 31st Jan 2017
Multidisciplinary development of selective anti-parasitic multi-target inhibitors of PTR1/DHFR based on a pteridine scaffold.
Submitter: Ina Poehner
Studies: Docking to PTR1 and DHFR targets and off-targets, In silico property and correlation analysis
Assays: Compound library preparation, Correlation analysis between PTR1 and DHFR activities and anti-parasitic..., Correlation analysis between predicted ADMET properties and anti-parasit..., Docking receptor preparation, In silico ADMET data prediction, Induced-fit docking studies, PAINS filtering, Rigid-body docking studies
Rigid-body docking studies and induced-fit docking studies of pteridine-based compounds to the target proteins TbPTR1, TbDHFR, LmPTR1, LmDHFR and the off-target hDHFR. For both PTR1 variants and human DHFR, conserved structural water sets were considered. Preparations of compound libraries and docking receptors are also covered.
Docking results of pteridine-based compounds in different target PTR1 and DHFR receptors and the off-target human DHFR when treating ligands as flexible and the protein receptors as a rigid-body.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
