This repository contains data and simulation input from the paper:

"Application of the ESMACS binding free energy protocol to a highly varied ligand dataset: lactate dehydogenase A", David W. Wright, Fouad Husseini, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, and Peter V. Coveney

Preprint DOI: 10.26434/chemrxiv.8398055

What follows is a brief description of the contents.

Naming conventions

During the preparation of the paper two naming conventions have been used - internally ligands were numbered sequentially (giving l1-l22) but to agree with the experimental publication [1] we numbered the ligands LDHA12, LDHA14-LDHA34.

[1] R. A. Ward, et al., J. Med. Chem., 2012, 55, 3285–3306, DOI:10.1021/jm201734r

We have named directories using a combination of both, e.g. l1-LDHA12. In the data files (all in tab separated value format) the columns ligname represented internal numbering and jan.id the LDHA prefixed numbering.

Directories

initial-structures ligand-inputs mmpbsa protein-inputs

initial-structures

Amber forcefield topology (prmtop) and coordinate (inpcrd and pdb) files for complexes of LDHA with each ligand.

protein-inputs

Contains the PDB used to create starting structures (based on chain A of 4BJX), including conserved water molecules.

ligand-inputs

Contains the information on the ligands used to initiate the project that led to the paper and ligand parameters used for simulations. This includes:

• Biological data: LDHA_biol_data.tsv
• Ligand structures: LDHA_ligands.sdf
• Forcefield parameters describing parameterized ligands, in Amber formats (frcmod and prep)
  • ligand_params_am1_bcc : Ligands using AM1-BCC charges
  • ligand_params_gaussian_resp : Ligands using Gaussian/RESP charges

mmpbsa

Files related to MMPBSA analysis in tab separated values format.

• input - contains the MMPBSA input file used for all analyses
• wsaa, normal_mode and variational-entropy contain data from teh three investigated entropic contributions.