Comparative electrostatic analysis of dinitroaniline-sensitive and -resistant tubulins
Creation of homology models of various tubulins from dinitroaniline-sensitive and -resistant species, and a comparative analysis of their electrostatic potential grids overall and in putative binding site regions using PIPSA (Protein Interaction Property Similarity Analysis).
SEEK ID: https://fairdomhub.org/assays/2060
Modelling analysis
Projects: NMTrypI - New Medicines for Trypanosomatidic Infections
Investigation: Antiparasitic dinitroaniline-ether phospholipid hybrids
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: Trypanosoma cruzi, Trypanosoma brucei, Leishmania infantum, Leishmania donovani, Leishmania major
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Created: 16th Feb 2023 at 11:27
Last updated: 24th Apr 2023 at 13:34
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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
Design, synthesis, computational studies and biological evaluation of antiparasitic dinitroaniline-ether phospholipid hybrids
Submitter: Ina Poehner
Studies: Computational identification of potential dinitroaniline binding sites i..., Docking studies of trifluraline and the dinitroaniline-etherphospholipid...
Assays: Comparative electrostatic analysis of dinitroaniline-sensitive and -resi..., Induced-fit docking studies, Multiple sequence alignment, Preparation of multimeric tubulin docking receptors
Sequence and electrostatic potential analyses to identify sites in tubulins that differ between dinitroaniline-sensitive and dinitroaniline-resistant species.
Collected PDB-files of homology models of alpha-tubulin, all based on T. thermophila tubulin PDB-ID 5ubq, chain A:
Includes models of the following dinitroaniline herbicide sensitive species (UniProt ID in brackets):
- C. reinhardtii (P09204)
- E. indica (O22347)
- L. donovani (I3W8N6)
- L. infantum (E9AGJ8)
- L. major (Q4QGC5)
- P. falciparum (P14642)
- S. viridis (Q65C79)
- T. brucei (Q4GYY5)
- T. cruzi (Q27352)
- T. gondii (P10873)
- Z. mays (P14640)
Includes models of the following dinitroaniline ...
This archive contains all results of the PIPSA analysis run in zipped form. It contains the following subfolders:
- apbs: Computed electrostatic potential grids, all log files and similarity matrices for the full protein and all sites.
- pdb2pqr: PQR files: conversion results after processing uploaded PDB files with pdb2pqr
- pdbs: Original uploaded PDB files
The following sites have been analyzed (provided are site center (based on T. cruzi model, Ca of the residue) and the sphere radius):
Blume ...
General SOP for the webPIPSA workflow to study electrostatic potential differences of full alpha-tubulin homology models and various putative binding site regions
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
General SOP for alpha-tubulin homology model building
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
SOP for protein preparation steps performed for alpha-tubulin homology models (hydrogen addition, hydrogen bonding network optimization and energy minimization)
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
