README.md

Article Title: Cholesterol derivatives regulate Adenylyl cyclase 7 activity by binding CARC and CRAC motifs in the cytosolic parts

Author: [Radim Jaroušek] [[email protected]]

Corresponding Author:[Lukas Kubala] [[email protected]]

This repository contains supplementary data, analysis scripts, and supporting files associated with the article "Cholesterol derivatives regulate Adenylyl cyclase 7 activity by binding CARC and CRAC motifs in the cytosolic parts"

Repository Structure

DeepSite -binding site prediction

Contains input files and results from DeepSite, a binding site prediction tool. These predictions helped identify potential cholesterol and derivative binding pockets on the AC7 structure.

DiffDock - DiffDock docking of cholesterol derivatives

Results obtained from DiffDock, a diffusion-based docking method. It includes configuration files, run scripts, and output data showing how cholesterol derivatives interact with the predicted AC7 binding sites.

DockThor_Cholesterol

Docking results using the DockThor platform. This directory holds input files, run parameters, and docking outputs to visualize and assess how cholesterol interacts with AC7 binding motifs.

Molecules - optimized structures of ligands

A collection of optimized 3D structures of cholesterol derivatives used as ligands. These have been geometry-optimized prior to docking experiments, ensuring more accurate predictions of ligand orientation and interaction.

MSA - Multiple sequence alignment of tmAC1-AC9 R script

Contains a script (Rmakrdown) and related files for generating and analyzing a multiple sequence alignment (MSA) of transmembrane Adenylyl Cyclases AC1 through AC9. This alignment provides comparative insights into CARC and CRAC motif conservation and variation across isoforms.

Optimized_AC7_AlphaFold

Files generated by refining the AlphaFold-predicted structure of AC7. These optimized models served as a starting point for identifying binding sites and conducting docking simulations.

Pymol_session - pymol object with cholesterol ligands and AC7 predicted structure

A PyMOL session file (.pse) that can be opened to visualize the AC7 structure, its cholesterol-binding sites, and docked ligand conformations. This provides an interactive 3D representation of the results.