This repository contains data and simulation input from the paper:

"Application of ESMACS binding free energy protocols to diverse datasets:Bromodomain-containing protein 4", David W. Wright, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Christophe Meyer, Gary Tresadern, and Peter V. Coveney

Preprint DOI: 10.26434/chemrxiv.7327019

What follows is a brief description of the contents

Naming conventions

Two models based on different crystal structrues were used to create the simulation starting structures, these are referred to by the PDB ascession numbers - 2oss and 4bjx.

Two ligand datasets are studied in this work, which are designated diverse (DIV) and tetrahydroquinoline scaffold (THQ).

DIV dataset is labelled J1-J12, this coresponds to ligands 1-11 in the paper (with J12 being the second pose of ligand 11).
THQ dataset is labelled G1-G16.

The naming reflects the origin of the datasets as coming from collaborations with Janssen and GSK respectively.

Directories

initial-pdbs

Contains the PDBS used to create starting structures, including conserved water molecules

ligand-ff-params

Forcefield files (frcmod and prep) describing parameterized ligands.

am1 - contains AM1-BCC parameters for the DIV ligands
gauss - contains all ligands parameterized using Gaussian/RESP method

mmpbsa

Files related to MMPBSA analysis in tab separated values format.

input - contains the MMPBSA input file used for all analyses
2oss and 4bjx - contain results for the two different starting structures

Within the two results directories sub-directories contain results calculated with differing numbers of explicit water molecules, labelled watX with X indicating the number of water molecules.

simulated-topologies

Amber forcefield topology (prmtop) and coordinate (inpcrd and pdb) files for all ligand for both the 2oss and 4bjx structures.