Published September 6, 2024
| Version 0.0.0
Data paper
Open
Mechanisms of Tecovirimat Antiviral Activity and Poxvirus Resistance (SI)
Authors/Creators
-
Vernuccio, Riccardo
(Researcher)1
-
Martínez León, Alejandro
(Data collector)2
-
Poojari, Chetan
(Researcher)2
-
Buchrieser, Julian
(Researcher)3
-
Selverian, Christopher
(Researcher)4
- Jaleta, Yakin (Researcher)4
- Meola, Annalisa (Researcher)1
-
Guivel-Benhassine, Florence
(Researcher)1
-
Porrot, Françoise
(Researcher)1
-
Haouz, Ahmed
(Researcher)5
- Chevreuil, Maelen (Researcher)1
-
Raynal, Bertrand3
- Mercer, Jason (Researcher)6
-
Simon-Loriere, Etienne
(Researcher)1
-
Chandran, Karti
(Researcher)7
-
Schwartz, Olivier
(Researcher)1
-
Hub, Jochen S.
(Researcher)2
- Guardado-Calvo, Pablo (Researcher)1
-
1.
Instituto Pasteur
-
2.
Saarland University
- 3. Institut Pasteur
-
4.
Albert Einstein College of Medicine
- 5. Plate-forme Cristallographie, Institut Pasteur
- 6. Birmingham University
- 7. Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
Description
Supporting information for the paper Mechanisms of Tecovirimat Antiviral Activity and Poxvirus Resistance
ABFE section
Monomer and dimmer simulations
archive.tar.gz
- - BindFLow-inputs: All the necesarry files to run BindFlow and obtain the reported results. Consider that 2 MD simulaitons are almost never the same.
- - fep-openff-2.0.0_light and fep-openff-2.0.0-monomer_light: Presents a minimalist set of files to reproduce the calculations for the dimmer and monomer respectivelly:
- Molecular Dynamic Parameters (MDP file) of each stage
- Topology files (TOP file)
- dh/dlambda for all perturbation (XVG file)
- Configuration files of key steps (GRO file)
- For each COMPLEX there is one directory ligand. Inisde of it you will find an input directory which have the TOP, GRO, NDX and ITP files necesary to perform the MD simulation. In the case of the complex simulations, you will find in all the replicas directories in complex/equil-mdsim/boreschcalc the GRO and TOP files that were used as input for the FEP complex simulaitons. Specifically in complex/fep/topology the topology of the complex after adding the boresch restraint information. The last topology is the real input for all FEP calculations in the complex.
Tables of final calculations (fep_results*)
Sumary tables of the calculations.
Files
fep_results_gather-dimmer.csv
Files
(7.2 GB)
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Additional details
Related works
- Is published in
- Publication: 10.21203/rs.3.rs-5002222/v1 (DOI)
Software
- Repository URL
- https://github.com/ale94mleon/BindFlow
- Programming language
- Python
- Development Status
- Active