Mechanisms of Tecovirimat Antiviral Activity and Poxvirus Resistance (SI)

Supporting information for the paper Mechanisms of Tecovirimat Antiviral Activity and Poxvirus Resistance F13 dimmer simulations in the membrane F13-Dimer_Membrane_Simulations.zip: Contains the starting and final structure files from MD simulations of the F13 dimer on a membrane that mimics Golgi-membrane composition. The file also includes the index.ndx, mdp, and topology files used in these simulations. Refinement of Tecovirimant conformation by RosettaEMERALD Ligand_Refinement_RosettaEMERALD.zip: Contains the files needed to reproduce the results are: docking.xml: Docking parameters flags: Flags used during docking TPOX.params: Tecovirimant's parameters. docking.xml and flags have and placeholders. These files can be downloaded from the structures deposited on the Protein Data Bank. 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 molecular dynamic 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. ABFE validation archive-ABFE-validation.tar.gz These simulations were conducted to validate our Absolute Binding Free Energy (ABFE) pipeline on this system. The directory mirrors the structure of archive.tar.gz and includes seven structurally similar tecovirimat ligands, as well as tecovirimat itself. References for the experimental data can be found at: Wang, J., Shahed-AI-Mahmud, M., Chen, A., Li, K., Tan, H., & Joyce, R. (2023). An overview of antivirals against monkeypox virus and other orthopoxviruses. Journal of medicinal chemistry, 66(7), 4468-4490. [Primary referen