SEEK ID: https://fairdomhub.org/people/666
ORCID:
https://orcid.org/0000-0002-2801-8902
Joined: 27th May 2016
Kinetics on the move - Workshop 2016 (Kinetics on the move Workshop at HITS) ; COVID-19 Disease Map (Heidelberg Institute for Theoretical Studies (HITS gGmbH)) ; NMTrypI - New Medicines for Trypanosomatidic Infections (Heidelberg Institute for Theoretical Studies (HITS gGmbH)) ; CoVIDD - Coronavirus interactions in drug discovery - optimization and implementation (University of Eastern Finland (UEF))
Related items
- Programmes (3)
- Projects (4)
- Institutions (3)
- Investigations (1)
- Studies (2)
- Assays (8)
- Data files (33)
- SOPs (5)
- Publications (10)
Projects: NMTrypI - New Medicines for Trypanosomatidic Infections
Web page: https://cordis.europa.eu/programme/id/FP7_HEALTH.2013.2.3.4-2
The Disease Maps Project is designed as a large-scale community effort. It is a network of groups that work together in order to better understand disease mechanisms. The project exchanges best practices, share information, develop tools to make it easier for all the involved groups to achieve their goals.
Projects: COVID-19 Disease Map
Web page: https://disease-maps.org
The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans). de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the ...
Projects: de.NBI-SysBio, ExtremoPharm, ZucAt, Kinetics on the move - Workshop 2016, Example use cases, MIX-UP, Working Group Nicole Radde, MPIEvolBio-SciComp
Web page: http://www.denbi.de
Here we share resources and best practices to develop a disease map for COVID-19. The project is progressing as a broad community-driven effort. We aim to establish a knowledge repository on virus-host interaction mechanisms specific to the SARS-CoV-2. The COVID-19 Disease Map is an assembly of molecular interaction diagrams established based on literature evidence.
Programme: Disease Maps
Public web page: http://doi.org/10.17881/covid19-disease-map
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
In the CoVIDD project, we aim at unravelling interactions of viral proteins with the cellular factors and the host pathways involved in SARS-CoV-2 infection by a combination of modern technologies, genomics, proteomics, structural biology, chemoinformatics and drug discovery. To effectively search for drugs that could modify viral replication we need to know what human proteins and viral proteins interact. Thus, a comprehensive virus-host protein interaction network will help us to identify the ...
Programme: This Project is not associated with a Programme
Public web page: Not specified
The workshop focuses on the publication, curation, retrieval, and usage of kinetic data from the reaction kinetics database SABIO-RK and on the use of data in modeling. There will be experience reports from scientists who successfully used experimental data to formulate or verify biological hypotheses with the computer, and you will experience how experimental data can be used with computational models.
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: http://www.h-its.org/event/kinetics-on-the-move/
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
Snapshots: No snapshots
Computational prediction of physicochemical and advanced descriptors related to ADME-Tox and PAINS assessment. Potential correlations of the computed descriptors with experimentally determined anti-parasitic activities and correlations between experimentally determined levels of target protein inhibition (PTR1, DHFR) with the anti-parasitic activity were also studied.
Submitter: Ina Poehner
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Assays: Correlation analysis between PTR1 and DHFR activities and anti-parasitic..., Correlation analysis between predicted ADMET properties and anti-parasit..., In silico ADMET data prediction, PAINS filtering
Snapshots: No snapshots
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.
Submitter: Ina Poehner
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Assays: Compound library preparation, Docking receptor preparation, Induced-fit docking studies, Rigid-body docking studies
Snapshots: No snapshots
Computational prediction of physicochemical and advanced descriptors related to ADME-Tox.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
SOPs: ADMET-property prediction SOP with QikProp
Data files: QikProp data for merged series compounds (serie..., QikProp data for pteridine in silico library, QikProp data for reference pteridines and N10-,...
Snapshots: No snapshots
Assessment of possible linear correlations between predicted ADMET descriptors from QikProp (Schrödinger, LLC, New York, NY) runs and experimentally determined activities against T. brucei brucei bloodstream forms with the help of a Python script.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Python module for calculating pairwise correlat...
Snapshots: No snapshots
Assessment of the possible multiple correlation between experimentally determined TbPTR1 and TbDHFR inhibition values and corresponding anti-parasitic activities against T. brucei brucei bloodstream forms using a Python script.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Python module for calculating trivariate statis...
Snapshots: No snapshots
In silico check and filtering for potential Pan-assay interference compounds.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: FAF-Drugs4 PAINS filtering results and addition...
Snapshots: No snapshots
Compound data, library construction schemes and preparation routine for small drug-like molecules as ligands in docking and for further analysis.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
SOPs: Ligand 3D structure preparation SOP
Data files: Fragments used for construction of the in silic..., SDF files of protonated pteridine compounds, SMILES strings for resynthesized and newly desi...
Snapshots: No snapshots
Prepared target (parasite PTR1, DHFR) and off-target (human DHFR) protein receptors for docking studies, in part with conserved structural water sets, and the corresponding preparation routine.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: Leishmania major, Trypanosoma brucei
Models: No Models
SOPs: Protein receptor preparation SOP for docking
Data files: LmDHFR docking receptor without water molecules, LmPTR1 docking receptor with conserved structur..., LmPTR1 docking receptor without water molecules, TbDHFR docking receptor without water molecules, TbPTR1 docking receptor with conserved structur..., TbPTR1 docking receptor without water molecules, hDHFR docking receptor with conserved structura..., hDHFR docking receptor without water
Snapshots: No snapshots
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...
Organisms: Leishmania major, Trypanosoma brucei
Models: No Models
SOPs: Rigid-body XP docking with Glide
Data files: PDB files of pteridine docking results in LmDHF..., PDB files of pteridine docking results in LmPTR..., PDB files of pteridine docking results in LmPTR..., PDB files of pteridine docking results in TbDHF..., PDB files of pteridine docking results in TbPTR..., PDB files of pteridine docking results in TbPTR..., PDB files of pteridine docking results in hDHFR..., PDB files of pteridine docking results in hDHFR...
Snapshots: No snapshots
Docking results of pteridine-based compounds in different target PTR1 and DHFR receptors and the off-target human DHFR when using an induced fit docking routine with an initial crude ligand placement step, subsequent receptor optimization in response to ligand binding and another docking step into the optimized receptor.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: Leishmania major, Trypanosoma brucei
Models: No Models
SOPs: Induced fit docking with Glide and Prime as par...
Data files: PDB files of induced fit docking results for se..., PDB files of induced fit docking results for se..., PDB files of induced fit docking results for se..., PDB files of induced fit docking results for se..., PDB files of induced fit docking results for th..., PDB files of induced fit docking results for th..., PDB files of induced fit docking results for th..., PDB files of induced fit docking results for th...
Snapshots: No snapshots
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the TbPTR1 receptor based on PDB-ID 2x9g without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the TbPTR1 receptor based on PDB-ID 2x9g with explicit conserved structural water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file. ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the TbDHFR receptor based on PDB-ID 3rg9 without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the LmPTR1 receptor based on PDB-ID 1e92 without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the LmPTR1 receptor based on PDB-ID 1e92 with explicit conserved structural water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file. ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the LmDHFR receptor based on the published homology model of LmDHFR (Panecka-Hofman et al. (2017) Biochim Biophys Acta Gen Subj. 1861(12), 3215-3230. DOI: 10.1016/j.bbagen.2017.09.012) without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the hDHFR receptor based on PDB-ID 1u72 without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the hDHFR receptor based on PDB-ID 1u72 with explicit conserved structural water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file. ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with induced fit docking results for reference compounds methotrexate and 1b as well as the N10-modified compounds 2a and 2e in their neutral and N1-protonated variants and the PABA-modified compound 3d in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The TbPTR1 receptor was based on PDB-ID 2x9g without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
Zip-archive with induced fit docking results for reference compounds methotrexate and 1b as well as the N10-modified compounds 2a and 2e in their neutral and N1-protonated variants and the N10-modified compound 2c and merged-series compound 5e in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The TbPTR1 receptor was based on PDB-ID 2x9g with explicit conserved structural water molecules. Docking results were obtained by Induced ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The TbDHFR receptor was based on PDB-ID 3rg9 without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced Fit Docking ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
Zip-archive with induced fit docking results for reference compounds methotrexate, 1b and 1c as well as the N10-modified compound 2e in their neutral and N1-protonated variants and the N10-modified compound 2a and Tail-modified compounds 4e, 4f, 4i and 4j in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The LmPTR1 receptor was based on PDB-ID 1e92 without additional water molecules. Docking results were obtained by Induced ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
Zip-archive with induced fit docking results for reference compounds methotrexate, 1b and 1c as well as the N10-modified compound 2e in their neutral and N1-protonated variants and the PABA-modified compound 3e in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The LmPTR1 receptor was based on PDB-ID 1e92 with explicit conserved structural water molecules. Docking results were obtained by Induced Fit docking with Schrödinger ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The LmDHFR receptor was based on a published homology model of LmDHFR (Panecka-Hofman et al. (2017) Biochim Biophys Acta Gen Subj. 1861(12), 3215-3230. DOI: 10.1016/j.bbagen.2017.09.012) without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The hDHFR receptor was based on PDB-ID 1u72 without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced Fit Docking ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The hDHFR receptor was based on PDB-ID 1u72 with explicit conserved structural water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
Compound SMILES of resynthesized or newly designed pteridine compounds 1b, 1c, 2a-e, 3a-e, 4a-j and 5a-f used for ligand preparation within Maestro (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Maestro.). SMILES strings and compound identifiers are comma-separated and can be readily imported in Maestro.
Creators: Ina Poehner, Antonio Quotadamo
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Compound library preparation
Zip archive of N1 protonated reference and newly synthesized pteridines (series 1-5) in SDF format.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Compound library preparation
Pteridines checked for Pan-assay interference compounds with the FAF-Drugs4 webserver (https://fafdrugs4.rpbs.univ-paris-diderot.fr/, last checked August 2020 and Lagorce et al. (2015) Nucleic Acids Res. 43, W200–207). Archive of PAINS filtering and ADME-Tox prediction results from FAF-Drugs4 run performed April 2019 with compound SMILES as input: applied_filters.txt: list of filters used; compound.sdf, accepted.sdf, intermediate.sdf, rejected.sdf, covalent_inhibitors.sdf and pains.sdf: compound ...
Creator: Ina Poehner
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: In silico property and correlation analysis
Assays: PAINS filtering
Results of default run of Schrödinger QikProp (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, QikProp v4.6.) for reference pteridines (series 1) and newly synthesized N10-, PABA and tail-modified pteridines (series 2, 3 and 4). QikProp in silico predicts various physico-chemical compound properties and advanced descriptors related to administration, distribution, metabolism, excretion and toxicity of the compounds.
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: In silico property and correlation analysis
Assays: In silico ADMET data prediction
This SOP describes the preparation of pteridine ligand 3D structures from SMILES or other input formats with the LigPrep routine as embedded in Schrödinger Maestro for usage in docking runs and in silico ADME-Tox property prediction.
Creators: Ina Poehner, Rebecca Wade, Joanna Panecka-Hofman
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Compound library preparation
This SOP describes the docking receptor preparation of PTR1 and DHFR receptor PDB files, performed with the Maestro Protein PrepWizard and the Glide grid generation routine. The optional identification and integration of conserved structural water molecules with the WatCH tool is also covered.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Docking receptor preparation
This SOP describes the in silico ADME-Tox property prediction with QikProp for prepared pteridine ligands.
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: In silico property and correlation analysis
Assays: In silico ADMET data prediction
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.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
This SOP describes the docking of pteridine libraries into PTR1 or DHFR target receptors, using Glide and Prime in Schrödinger Maestro as part of the Induced Fit workflow to allow for receptor side chain reorganization upon ligand binding.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
Abstract (Expand)
Authors: Zlatka Plavec, Ina Pöhner, Antti Poso, Sarah J Butcher
Date Published: 1st Dec 2021
Publication Type: Journal
DOI: 10.1016/j.coviro.2021.09.005
Citation: Current Opinion in Virology 51:16-24
Abstract (Expand)
Authors: Xiaonan Liu, Sini Huuskonen, Tuomo Laitinen, Taras Redchuk, Mariia Bogacheva, Kari Salokas, Ina Pöhner, Tiina Öhman, Arun Kumar Tonduru, Antti Hassinen, Lisa Gawriyski, Salla Keskitalo, Maria K Vartiainen, Vilja Pietiäinen, Antti Poso, Markku Varjosalo
Date Published: 1st Nov 2021
Publication Type: Journal
Citation: Mol Syst Biol 17(11)
Abstract (Expand)
Authors: P. Linciano, C. Pozzi, L. D. Iacono, F. di Pisa, G. Landi, A. Bonucci, S. Gul, M. Kuzikov, B. Ellinger, G. Witt, N. Santarem, C. Baptista, C. Franco, C. B. Moraes, W. Muller, U. Wittig, R. Luciani, A. Sesenna, A. Quotadamo, S. Ferrari, I. Pohner, A. Cordeiro-da-Silva, S. Mangani, L. Costantino, M. P. Costi
Date Published: 25th Apr 2019
Publication Type: Journal
PubMed ID: 30908048
Citation: J Med Chem. 2019 Apr 25;62(8):3989-4012. doi: 10.1021/acs.jmedchem.8b02021. Epub 2019 Apr 9.
Abstract (Expand)
Authors: C. B. Moraes, G. Witt, M. Kuzikov, B. Ellinger, T. Calogeropoulou, K. C. Prousis, S. Mangani, F. Di Pisa, G. Landi, L. D. Iacono, C. Pozzi, L. H. Freitas-Junior, B. Dos Santos Pascoalino, C. P. Bertolacini, B. Behrens, O. Keminer, J. Leu, M. Wolf, J. Reinshagen, A. Cordeiro-da-Silva, N. Santarem, A. Venturelli, S. Wrigley, D. Karunakaran, B. Kebede, I. Pohner, W. Muller, J. Panecka-Hofman, R. C. Wade, M. Fenske, J. Clos, J. M. Alunda, M. J. Corral, E. Uliassi, M. L. Bolognesi, P. Linciano, A. Quotadamo, S. Ferrari, M. Santucci, C. Borsari, M. P. Costi, S. Gul
Date Published: 21st Feb 2019
Publication Type: Journal
PubMed ID: 30784368
Citation: SLAS Discov. 2019 Mar;24(3):346-361. doi: 10.1177/2472555218823171.
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Authors: P. Linciano, A. Dawson, I. Pohner, D. M. Costa, M. S. Sa, A. Cordeiro-da-Silva, R. Luciani, S. Gul, G. Witt, B. Ellinger, M. Kuzikov, P. Gribbon, J. Reinshagen, M. Wolf, B. Behrens, V. Hannaert, P. A. M. Michels, E. Nerini, C. Pozzi, F. di Pisa, G. Landi, N. Santarem, S. Ferrari, P. Saxena, S. Lazzari, G. Cannazza, L. H. Freitas-Junior, C. B. Moraes, B. S. Pascoalino, L. M. Alcantara, C. P. Bertolacini, V. Fontana, U. Wittig, W. Muller, R. C. Wade, W. N. Hunter, S. Mangani, L. Costantino, M. P. Costi
Date Published: 30th Sep 2017
Publication Type: Journal
PubMed ID: 28983525
Citation: ACS Omega. 2017 Sep 30;2(9):5666-5683. doi: 10.1021/acsomega.7b00473. Epub 2017 Sep 11.
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Authors: J. Panecka-Hofman, I. Pohner, F. Spyrakis, T. Zeppelin, F. Di Pisa, L. Dello Iacono, A. Bonucci, A. Quotadamo, A. Venturelli, S. Mangani, M. P. Costi, R. C. Wade
Date Published: 25th Sep 2017
Publication Type: Journal
PubMed ID: 28939533
Citation: Biochim Biophys Acta Gen Subj. 2017 Dec;1861(12):3215-3230. doi: 10.1016/j.bbagen.2017.09.012. Epub 2017 Sep 20.
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Authors: W. Jedwabny, J. Panecka-Hofman, E. Dyguda-Kazimierowicz, R. C. Wade, W. A. Sokalski
Date Published: 9th Jul 2017
Publication Type: Journal
PubMed ID: 28688090
Citation: J Comput Aided Mol Des. 2017 Aug;31(8):715-728. doi: 10.1007/s10822-017-0035-4. Epub 2017 Jul 7.
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Authors: A. Stank, D. B. Kokh, M. Horn, E. Sizikova, R. Neil, J. Panecka, S. Richter, R. C. Wade
Date Published: 3rd Jul 2017
Publication Type: Journal
PubMed ID: 28431137
Citation: Nucleic Acids Res. 2017 Jul 3;45(W1):W325-W330. doi: 10.1093/nar/gkx277.
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Authors: F. Di Pisa, G. Landi, L. Dello Iacono, C. Pozzi, C. Borsari, S. Ferrari, M. Santucci, N. Santarem, A. Cordeiro-da-Silva, C. B. Moraes, L. M. Alcantara, V. Fontana, L. H. Freitas-Junior, S. Gul, M. Kuzikov, B. Behrens, I. Pohner, R. C. Wade, M. P. Costi, S. Mangani
Date Published: 8th Mar 2017
Publication Type: Journal
PubMed ID: 28282886
Citation: Molecules. 2017 Mar 8;22(3). pii: molecules22030426. doi: 10.3390/molecules22030426.
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Authors: C. Borsari, R. Luciani, C. Pozzi, I. Poehner, S. Henrich, M. Trande, A. Cordeiro-da-Silva, N. Santarem, C. Baptista, A. Tait, F. Di Pisa, L. Dello Iacono, G. Landi, S. Gul, M. Wolf, M. Kuzikov, B. Ellinger, J. Reinshagen, G. Witt, P. Gribbon, M. Kohler, O. Keminer, B. Behrens, L. Costantino, P. Tejera Nevado, E. Bifeld, J. Eick, J. Clos, J. Torrado, M. D. Jimenez-Anton, M. J. Corral, J. M. Alunda, F. Pellati, R. C. Wade, S. Ferrari, S. Mangani, M. P. Costi
Date Published: 25th Aug 2016
Publication Type: Journal
PubMed ID: 27411733
Citation: J Med Chem. 2016 Aug 25;59(16):7598-616. doi: 10.1021/acs.jmedchem.6b00698. Epub 2016 Aug 5.