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The reactions existing in the auto-generated draft model are shown in blue, and the manually filled gaps are shown in green. Comparing our draft model with the same subsystem from model iHepatocytes2322, the missing reactions are highlighted in pink. The pink dots indicate the parent toxicants.

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Creator: Xiaokang Zhang

Submitter: Xiaokang Zhang

Creator: Xiaokang Zhang

Submitter: Xiaokang Zhang

COBRA Matlab toolbox was used.

Small set of values for entering into NetLogo simulation

Zip-archive with induced fit docking results for reference compounds methotrexate, 1 and 2 as well as the N10-modified compound 4 in their neutral and N1-protonated variants and the N10-modified compound 3 and Tail-modified compounds 14, 16, 17 and 26 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 Fit
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Zip-archive with induced fit docking results for reference compounds methotrexate and 1 as well as the N10-modified compounds 3 and 4 in their neutral and N1-protonated variants and the N10-modified compound 9 and merged-series compound 19 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
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Zip-archive with induced fit docking results for reference compounds methotrexate and 1 as well as the N10-modified compounds 3 and 4 in their neutral and N1-protonated variants and the PABA-modified compound 27 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 Prime
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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.
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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.

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.

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.
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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.

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
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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
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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
...

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
...

Zip-archive with induced fit docking results for reference compounds methotrexate, 1 and 2 as well as the N10-modified compound 4 in their neutral and N1-protonated variants and the PABA-modified compound 28 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 Glide
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PDB file of the prepared human dihydrofolate reductase docking receptor based on chain A of PDB-ID 1u72 with a conserved set of structural waters.

PDB file of the prepared human dihydrofolate reductase docking receptor based on chain A of PDB-ID 1u72 without additional water molecules.

PDB file of the prepared Leishmania major dihydrofolate reductase docking receptor 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 water molecules.

PDB file of the prepared Leishmania major pteridine reductase 1 docking receptor based on chain A of PDB-ID 1e92 with a conserved set of structural waters.

PDB file of the prepared Leishmania major pteridine reductase 1docking receptor based on chain A of PDB-ID 1e92 without additional water molecules.

PDB file of the prepared Trypanosoma brucei dihydrofolate reductase docking receptor based on chain A of PDB-ID 3rg9 without water molecules.

PDB file of the prepared Trypanosoma brucei pteridine reductase 1 docking receptor based on chain A of PDB-ID 2x9g with a conserved set of structural waters.

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