Uni-GBSA: An Automatic Workflow to Perform MM/GB(PB)SA Calculations for Virtual Screening

[Briefings in Bioinformatics]

Background

Calculating the binding free energy of a ligand to a protein receptor is a crucial goal in drug discovery. Molecular mechanics/Generalized-Born (Poisson-Boltzmann) surface area (MM/GB(PB)SA), which balances accuracy and efficiency, is one of the most widely used methods for evaluating ligand binding free energies in virtual screening. Uni-GBSA is an automatic workflow to perform MM/GB(PB)SA calculations. It includes several functions, including but not limited to topology preparation, structure optimization, binding free energy calculation, and parameter scanning for MM/GB(PB)SA calculations. Additionally, it has a batch mode that allows the evaluation of thousands of molecules against one protein target simultaneously, enabling its application in virtual screening.

Install

Install via Conda

To run uni-GBSA, you need to install several third-party softwares including acpype, gmxMMPBSA, lickit, etc. ```Bash conda create -n gbsa -c conda-forge acpype openmpi mpi4py gromacs "gmxmmpbsa>=1.5.6" conda activate gbsa pip install unigbsa lickit ```

Install by docker images

You can also build a docker image using this file or pull from the docker hub docker pull dockerymh/unigbsa ```Plaintext FROM continuumio/miniconda3

1. create an environment

SHELL ["/bin/bash", "-c"] RUN conda create -n gbsa -c conda-forge acpype openmpi mpi4py gromacs "gmx_MMPBSA>=1.5.6" \ && echo 'conda activate gbsa' >> ~/.bashrc \ && rm -rf /opt/conda/pkgs/*

2. install unigbsa

RUN source ~/.bashrc \ && pip install unigbsa lickit \ && rm -rf ~/.cache/*

```

Usage & Example

Usage

```bash $ unigbsa-pipeline -h usage: unigbsa-pipeline [-h] -i RECEPTOR [-l LIGAND [LIGAND ...]] [-c CONFIG] [-d LIGDIR] [-f PBSAFILE] [-o OUTFILE] [-validate] [-nt THREADS] [--decomp] [--verbose] [-v]

MM/GB(PB)SA Calculation. Version: 0.1.6

optional arguments: -h, --help show this help message and exit -i RECEPTOR Input protein file in pdb format. -l LIGAND [LIGAND ...] Ligand files to calculate binding energy for. -c CONFIG Config file, default: /home/jochem/miniforge3/envs/gbsatest/lib/python3.9/site-packages/unigbsa/data/default.ini -d LIGDIR Directory containing many ligand files. file format: .mol or .sdf -f PBSAFILE gmxMMPBSA input file. default=None -o OUTFILE Output file. -validate Validate the ligand file. default: False -nt THREADS Set number of threads to run this program. --decomp Decompose the free energy. default:False --verbose Keep all the files. -v, --version show program's version number and exit ```

Example

```bash $ unigbsa-pipeline -i example/1ceb/1cebprotein.pdb -l example/1ceb/1cebligand.sdf -o BindingEnergy.csv

07/07/2024 15:56:01 PM - INFO - Build protein topology. 07/07/2024 15:56:02 PM - INFO - Build ligand topology: 1cebligand 07/07/2024 15:56:03 PM - INFO - Running energy minimization: 1cebligand 07/07/2024 15:56:04 PM - INFO - Run the MMPB(GB)SA.

07/07/2024 15:56:12 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode delta_G(kcal/mole) 1 gb -20.1781
```

Other Tools

This packge contains several commands: unigbsa-scan, unigbsa-pipeline, unigbsa-traj, unigbsa-pbc, unigbsa-buildtop, unigbsa-buildsys, unigbsa-md.

unigbsa-scan

Perform an automatic parameter optimization prior to production MM/GB(PB)SA calculations. ```Bash $ unigbsa-scan -h usage: unigbsa-scan [-h] [-i RECEPTOR] [-pd PROTDIR] [-l LIGAND [LIGAND ...]] [-ld LIGDIR] -e E -c PARASFILE [-o OUTDIR] [-nt THREADS] [--verbose]

Perform an automatic parameter optimization prior to production MM/GB(PB)SA calculations.

optional arguments: -h, --help show this help message and exit -i RECEPTOR Input protein file in pdb format. -pd PROTDIR Directory containing many protein files. file format: .pdb -l LIGAND [LIGAND ...] Ligand files to calculate binding energy. -ld LIGDIR Directory containing many ligand files. file format: .mol or .sdf -e E Experiment data file. -c PARASFILE Parameters to scan -o OUTDIR Output directory. -nt THREADS Set number of threads to run this program. --verbose Keep all the files. ```

Example Bash unigbsa-scan -i example/scan/protein.pdb -ld example/scan/ -e example/scan/ligands.csv -c example/scan/scan.json -o scan-demo -nt 4

unigbsa-pipeline

A simple, automatic pipeline to perform MM/GB(PB)SA calculations. You only need to provide a protein file (in the PDB format) and ligand files (in the MOL or SDF format). This function will perform an energy minimization then calculate the PBSA/GBSA values for the each input ligand.

• If you want perform energy minimization or MD simulation for the complex automatically, use the unigbsa-pipeline function. ```Bash $ unigbsa-pipeline -h usage: unigbsa-pipeline [-h] -i RECEPTOR [-l LIGAND [LIGAND ...]] [-c CONFIG] [-d LIGDIR] [-f PBSAFILE] [-o OUTFILE] [-validate] [-nt THREADS] [--decomp] [--verbose] [-v]

MM/GB(PB)SA Calculation. Version: 0.1.6

optional arguments: -h, --help show this help message and exit -i RECEPTOR Input protein file in pdb format. -l LIGAND [LIGAND ...] Ligand files to calculate binding energy for. -c CONFIG Config file, default: default.ini -d LIGDIR Directory containing many ligand files. file format: .mol or .sdf -f PBSAFILE gmx_MMPBSA input file. default=None -o OUTFILE Output file. -validate Validate the ligand file. default: False -nt THREADS Set number of threads to run this program. --decomp Decompose the free energy. default:False --verbose Keep all the files. -v, --version show program's version number and exit ```

You can change the parameters for the MM/GB(PB)SA calculations by providing a config file (default.ini). ``` ; parameters for simulation [simulation] ; input pose process method: ; input - just use input pose to calculation ; em - run a simple energy minimizaion for the input poses ; md - run a md simulation for the input poses mode = em

; simulation box type: triclinic, cubic, dodecahedron, octahedron boxtype = triclinic

; Distance between the solute and the simulation box boxsize = 0.9

; Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration conc = 0.15

; number of md simulation steps nsteps = 500000

; number of equilibrium simulation(nvt, npt) steps eqsteps = 50000

; number of structure to save for the md simulation nframe = 100

; protein forcefield (gromacs engine) proteinforcefield = amber03

; ligand forcefield (acpype engine) ligandforcefield = gaff ; ligand charge method: bcc, gas ligandCharge = bcc

; parameters for PBSA/GBSA calculation, support all the gmxMMPBSA parameters [GBSA] ; calculation name sysname = GBSA

; calculation mode, Separated by commas. gb,pb,decomposition modes = gb

; best parameters for PBSA/GBSA calculations obtained from Wang, Ercheng, et al. Chemical reviews 119.16 (2019): 9478-9508. igb = 2 indi = 4.0 exdi = 80.0 ```

unigbsa-traj

Perform a PBSA/GBSA calculation of a complex from a MD trajectory. Note: you need to prepare a gromacs index.ndx file which contains two groups named RECEPTOR and LIGAND.

```` $ unigbsa-traj -h usage: unigbsa-traj [-h] -i INP -p TOP -ndx NDX [-m MODE [MODE ...]] [-f MMPBSAFILE] [-t TRAJ] [-nt THREADS] [-D] [-v]

Free energy calcaulation by MM/GB(PB)SA method.

optional arguments: -h, --help show this help message and exit -i INP A pdb file or a tpr file for the trajectory. -p TOP Gromacs topol file for the system. -ndx NDX Gromacs index file, must contain receptor and ligand group. -m MODE [MODE ...] MM/GB(PB)SA mode -f MMPBSAFILE Input MM/GB(PB)SA file -t TRAJ A trajectory file containing many structure frames. File format: xtc, pdb, gro... -nt THREADS Set number of threads to run this program. -D DEBUG model, keep all the files. -v, --version show program's version number and exit

````

unigbsa-buildtop

Topology preparation for a protein receptor and ligand(s) using gromacs. ```Bash $ unigbsa-buildtop -h usage: unigbsa-buildtop [-h] [-p PROTEIN] [-l LIGAND] [-pf PROTFORCE] [-lf {gaff,gaff2}] [-o OUTDIR] [-c] [-nt THREADS] [-verbose] [-v]

Build topology file for input file.

optional arguments: -h, --help show this help message and exit -p PROTEIN Protein file or directory to build topology. -l LIGAND Ligand file or directory to build topology. -pf PROTFORCE Protein forcefield. -lf {gaff,gaff2} Ligand forcefield: gaff or gaff2. -o OUTDIR The output directory. -c Combine the protein and ligand topology. Suppport for one protein and more ligands. default:True -nt THREADS Number of threads to run this simulation. -verbose Keep the directory or not. -v, --version show program's version number and exit ```

unigbsa-buildsys

Build a simulation box for a protein-ligand complex. ```bash $ unigbsa-buildsys -h usage: unigbsa-buildsys [-h] -p PROTEIN [-l LIGAND] [-pf PROTFORCE] [-lf {gaff,gaff2}] [-bt BOXTYPE] [-box BOX BOX BOX] [-d D] [-conc CONC] [-o OUTDIR] [-nt THREADS] [-v]

Build MD simulation for input file.

optional arguments: -h, --help show this help message and exit -p PROTEIN Protein file for the simulation. -l LIGAND Ligand file or directory for the simulation. -pf PROTFORCE Protein forcefield. -lf {gaff,gaff2} Ligand forcefield: gaff or gaff2. -bt BOXTYPE Simulation box type, default: triclinic -box BOX BOX BOX Simulation box size. -d D Distance between the solute and the box. -conc CONC Specify salt concentration (mol/liter). default=0.15 -o OUTDIR The output directory. -nt THREADS Number of threads to run this simulation. -v, --version show program's version number and exit ```

unigbsa-md

Run a MD simulation of a protein-ligand complex. ```Bash $ unigbsa-md -h usage: unigbsa-md [-h] -p PROTEIN [-l LIGAND] [-pf PROTFORCE] [-lf {gaff,gaff2}] [-bt BOXTYPE] [-box BOX BOX BOX] [-d D] [-conc CONC] [-o OUTDIR] [-nsteps NSTEP] [-nframe NFRAME] [-nt THREADS] [-verbose] [-v]

Run MD simulation for input file.

optional arguments: -h, --help show this help message and exit -p PROTEIN Protein file for the simulation. -l LIGAND Ligand file or directory for the simulation. -pf PROTFORCE Protein forcefield. -lf {gaff,gaff2} Ligand forcefield: gaff or gaff2. -bt BOXTYPE Simulation box type, default: triclinic -box BOX BOX BOX Simulation box size. -d D Distance between the solute and the box. -conc CONC Specify salt concentration (mol/liter). default=0.15 -o OUTDIR The output directory. -nsteps NSTEP Simulation steps. default:2500 -nframe NFRAME Number of frames to save for the xtc file. default:100 -nt THREADS Number of threads to run this simulation. -verbose Keep all the files in the simulation. -v, --version show program's version number and exit ```

unigbsa-pbc

Process PBC condition for a MD trajectory. ```Bash $ unigbsa-pbc -h usage: unigbsa-pbc [-h] -s TPR -f XTC [-o OUT] [-n NDX] [-v]

Auto process PBC for gromacs MD trajectory.

optional arguments: -h, --help show this help message and exit -s TPR TPR file generated from gromacs or coordinate file. -f XTC Trajectory file to process PBC. -o OUT Results file after processed PBC. -n NDX Index file contains the center and output group. -v, --version show program's version number and exit ```

More Examples

• Perform a MM/GB(PB)SA calculation on a ligand file with a protein receptor with unigbsa-pipeline Bash unigbsa-pipeline -i ./example/2fvy/protein.pdb -l ./example/2fvy/BGC.mol2

• Perform a MM/GB(PB)SA calculation of a complex from a MD trajectory with unigbsa-traj Bash unigbsa-traj -i example/3f/complex.pdb -p example/3f/complex.top -ndx example/3f/index.ndx -m pb gb -t example/3f/complex.pdb

• Build topology for a protein receptor and a ligand using gromacs. unigbsa-buildtop bash unigbsa-buildtop -p example/2fvy/protein.pdb -pf amber99sb -o topol # build gromacs topology for a single protein unigbsa-buildtop -p example/2fvy/protein.pdb -pf amber99sb -l example/2fvy/BGC.mol2 -lf gaff -o 2fvy_topol -c # build gromacs topology for protein and ligand complex

• Build a simulation system with unigbsa-buildsys

• Run a MD simulation with unigbsa-md

• Process the PBC condition of a MD trajectory with unigbsa-pbc

Citation

plaintext Maohua Yang and others, Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening, Briefings in Bioinformatics, 2023;, bbad218, https://doi.org/10.1093/bib/bbad218.