LightDock

https://lightdock.org/tutorials/0.9.3/
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LightDock is a protein-protein, protein-peptide and protein-DNA docking protocol based on the...
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### LightDock Setup Output Example

Source: https://lightdock.org/tutorials/0.9.3/membrane

This output shows the typical log messages during the LightDock setup process, including warnings about incomplete sidechains and confirmation of file processing.

```text
[lightdock3_setup] INFO: Ignoring OXT atoms
[lightdock3_setup] INFO: Ignoring Hydrogen atoms
[lightdock3_setup] INFO: Reading structure from 3x29_receptor_membrane.pdb PDB file...
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue GLN.61
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue GLN.63
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue LYS.65
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue LEU.66
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue ASP.68
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue HIS.76
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue MET.95
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue MET.102
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue LYS.103
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue LYS.115
[pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue ARG.117
[lightdock3_setup] INFO: 1608 atoms, 601 residues read.
[lightdock3_setup] INFO: Ignoring OXT atoms
[lightdock3_setup] INFO: Ignoring Hydrogen atoms
[lightdock3_setup] INFO: Reading structure from 3x29_ligand.pdb PDB file...
[lightdock3_setup] INFO: 933 atoms, 117 residues read.
[lightdock3_setup] INFO: Calculating reference points for receptor 3x29_receptor_membrane.pdb...
[lightdock3_setup] INFO: Reference points for receptor found, skipping
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: Calculating reference points for ligand 3x29_ligand.pdb...
[lightdock3_setup] INFO: Reference points for ligand found, skipping
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: Saving processed structure to PDB file...
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: Saving processed structure to PDB file...
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: Calculating starting positions...
[lightdock3_setup] INFO: Generated 62 positions files
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: Number of calculated swarms is 62
[lightdock3_setup] INFO: Preparing environment
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: LightDock setup OK
```

--------------------------------

### LightDock Setup Output Example

Source: https://lightdock.org/tutorials/0.9.3/restraints

This output shows the successful execution of the LightDock setup, including reading structures, calculating reference points, processing restraints, and generating initial swarm positions.

```text
@> ProDy is configured: verbosity='info'
[lightdock_setup] INFO: Reading structure from 4G6M_rec.pdb PDB file...
[lightdock_setup] INFO: 1782 atoms, 230 residues read.
[lightdock_setup] INFO: Reading structure from 4G6M_lig.pdb PDB file...
[lightdock_setup] INFO: 1194 atoms, 149 residues read.
[lightdock_setup] INFO: Calculating reference points for receptor 4G6M_rec.pdb...
[lightdock_setup] INFO: Done.
[lightdock_setup] INFO: Calculating reference points for ligand 4G6M_lig.pdb...
[lightdock_setup] INFO: Done.
[lightdock_setup] INFO: Saving processed structure to PDB file...
[lightdock_setup] INFO: Done.
[lightdock_setup] INFO: Saving processed structure to PDB file...
[lightdock_setup] INFO: Done.
[lightdock_setup] INFO: 10 normal modes calculated
[lightdock_setup] INFO: 10 normal modes calculated
[lightdock_setup] INFO: Reading restraints from restraints.list
[lightdock_setup] INFO: Number of receptor restraints is: 20 (active), 0 (passive)
[lightdock_setup] INFO: Number of ligand restraints is: 21 (active), 0 (passive)
[lightdock_setup] INFO: Calculating starting positions...
[lightdock_setup] INFO: Generated 55 positions files
[lightdock_setup] INFO: Done.
[lightdock_setup] INFO: Number of swarms is 55 after applying restraints
[lightdock_setup] INFO: Preparing environment
[lightdock_setup] INFO: Done.
[lightdock_setup] INFO: LightDock setup OK

```

--------------------------------

### Run LightDock Rust Docking Simulation

Source: https://lightdock.org/tutorials/0.9.3/rust

Execute a real docking example using the lightdock-rust binary. This command initiates a docking simulation from a specified setup file.

```bash
cd example/1ppe
time ../../target/release/lightdock-rust setup_1ppe.json initial_positions_0.dat 100 dfire

```

--------------------------------

### LightDock Setup Command Help

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

Displays the usage information for the `lightdock3_setup` command, outlining available arguments and options.

```bash
usage: lightdock3_setup [-h] [-s SWARMS] [-g GLOWWORMS] [--seed_points STARTING_POINTS_SEED] [--noxt] [--noh] [--now]
                        [--verbose_parser] [-anm] [--seed_anm ANM_SEED] [--anm_rec_rmsd ANM_REC_RMSD]
                        [--anm_lig_rmsd ANM_LIG_RMSD] [-ar ANM_REC] [-al ANM_LIG] [-r restraints] [-membrane]
                        [-transmembrane] [-sp] [-sd SURFACE_DENSITY] [-sr SWARM_RADIUS] [-flip] [-fd FIXED_DISTANCE]
                        [-spr SWARMS_PER_RESTRAINT] [--ds] [-V]
                        receptor_pdb_file ligand_pdb_file
lightdock3_setup: error: the following arguments are required: receptor_pdb_file, ligand_pdb_file
```

--------------------------------

### LightDock Setup Output

Source: https://lightdock.org/tutorials/0.9.3/dna_docking

This is the expected output when the `lightdock3_setup.py` script runs successfully. It confirms the reading of structures, calculation of reference points, ANM, and restraints, and the generation of starting positions.

```text
@> ProDy is configured: verbosity='none'
[lightdock3_setup] INFO: Reading structure from protein.pdb PDB file...
[lightdock3_setup] INFO: 1094 atoms, 66 residues read.
[lightdock3_setup] INFO: Reading structure from dna.pdb PDB file...
[lightdock3_setup] INFO: 506 atoms, 16 residues read.
[lightdock3_setup] INFO: Calculating reference points for receptor protein.pdb...
[lightdock3_setup] INFO: Reference points for receptor found, skipping
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: Calculating reference points for ligand dna.pdb...
[lightdock3_setup] INFO: Reference points for ligand found, skipping
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: Saving processed structure to PDB file...
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: Saving processed structure to PDB file...
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: Calculating ANM for receptor molecule...
[lightdock3_setup] INFO: 10 normal modes calculated
[lightdock3_setup] INFO: Calculating ANM for ligand molecule...
[lightdock3_setup] INFO: 10 normal modes calculated
[lightdock3_setup] INFO: Reading restraints from restraints.list
[lightdock3_setup] INFO: Number of receptor restraints is: 3 (active), 0 (passive)
[lightdock3_setup] INFO: Number of ligand restraints is: 0 (active), 0 (passive)
[lightdock3_setup] INFO: Calculating starting positions...
[lightdock3_setup] INFO: Generated 21 positions files
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: Number of calculated swarms is 21
[lightdock3_setup] INFO: Preparing environment
[lightdock3_setup] INFO: Done.
[lightdock3_setup] INFO: LightDock setup OK

```

--------------------------------

### Install Rust Environment with rustup

Source: https://lightdock.org/tutorials/0.9.3/rust

Use this command to install the Rust compiler and cargo package manager. Follow the instructions on the rustup website for detailed setup.

```bash
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

```

--------------------------------

### Run LightDock Setup Script

Source: https://lightdock.org/tutorials/0.9.3/dna_docking

Execute the setup script with protein and DNA PDB files, enabling ANM and restraints. Ensure the restraints file is correctly specified.

```bash
lightdock3_setup.py protein.pdb dna.pdb -anm -rst restraints.list

```

--------------------------------

### LightDock Simulation Output Example

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

Shows the typical output generated during a LightDock simulation, including setup information, progress of steps, and completion messages. This helps in monitoring the simulation's progress.

```text
@> ProDy is configured: verbosity='info'
[lightdock3_setup] INFO: Ignoring OXT atoms
[lightdock3_setup] INFO: Ignoring Hydrogen atoms
[lightdock3_setup] INFO: Ignoring water
[lightdock3_setup] INFO: Reading structure from lightdock_2UUY_rec.pdb PDB file...
[lightdock3_setup] INFO: 1628 atoms, 223 residues read.
[lightdock3_setup] INFO: Ignoring OXT atoms
[lightdock3_setup] INFO: Ignoring Hydrogen atoms
[lightdock3_setup] INFO: Ignoring water
[lightdock3_setup] INFO: Reading structure from lightdock_2UUY_lig.pdb PDB file...
[lightdock3_setup] INFO: 415 atoms, 55 residues read.
[lightdock] INFO: Loading scoring function...
[lightdock] INFO: Using DFIRE scoring function
[lightdock] INFO: Done.
[kraken] INFO: Kraken has 1 tentacles (cpu cores)
[kraken] INFO: Tentacle ready with 1 tasks
[kraken] INFO: 1 ships ready to be smashed
[lightdock] INFO: Monster spotted
[kraken] INFO: Release the Kraken!
[0] step 1
[0] step 2
[0] step 3
[0] step 4
[0] step 5
[0] step 6
[0] step 7
[0] step 8
[0] step 9
[0] step 10
...
[0] step 100
[kraken] INFO: folding tentacle Tentacle-1
[kraken] INFO: 1 ships destroyed
[lightdock] INFO: Finished.
```

--------------------------------

### Run LightDock Setup with Restraints

Source: https://lightdock.org/tutorials/0.9.3/restraints

Execute the setup script with receptor and ligand PDB files, specifying options to exclude terminal oxygens, hydrogens, and water, enable normal modes, and apply residue restraints from a list.

```bash
lightdock3_setup.py 4G6M_rec.pdb 4G6M_lig.pdb --noxt --noh --now -anm -rst restraints.list

```

--------------------------------

### LightDock Setup Command Usage

Source: https://lightdock.org/tutorials/0.9.3/membrane

This shows the usage information for the `lightdock3_setup` command, including required arguments and available optional flags for customization.

```text
usage: lightdock3_setup [-h] [-s SWARMS] [-g GLOWWORMS] [--seed_points STARTING_POINTS_SEED] [--noxt] [--noh] [--verbose_parser] [-anm] [--seed_anm ANM_SEED] [-ar ANM_REC]
                        [-al ANM_LIG] [-r restraints] [-membrane] [-transmembrane] 
                        [-sp] [-sd SURFACE_DENSITY] [-sr SWARM_RADIUS]
                        receptor_pdb_file ligand_pdb_file
lightdock3_setup: error: the following arguments are required: receptor_pdb_file, ligand_pdb_file
```

--------------------------------

### LightDock Setup Command-Line Interface

Source: https://lightdock.org/tutorials/0.9.3/basics

This snippet shows the usage and required arguments for the `lightdock3_setup.py` script. It highlights the mandatory receptor and ligand PDB file inputs.

```bash
usage: lightdock3_setup [-h] [-s SWARMS] [-g GLOWWORMS] [--seed_points STARTING_POINTS_SEED] [--noxt]
                        [--noh] [--now] [--verbose_parser] [-anm] [--seed_anm ANM_SEED]
                        [--anm_rec_rmsd ANM_REC_RMSD] [--anm_lig_rmsd ANM_LIG_RMSD] [-ar ANM_REC]
                        [-al ANM_LIG] [-r restraints] [-membrane] [-transmembrane] [-sp]
                        [-sd SURFACE_DENSITY] [-sr SWARM_RADIUS] [-flip] [-fd FIXED_DISTANCE]
                        [-spr SWARMS_PER_RESTRAINT] [--ds]
                        receptor_pdb_file ligand_pdb_file
lightdock3_setup: error: the following arguments are required: receptor_pdb_file, ligand_pdb_file
```

--------------------------------

### Run LightDock Setup Script

Source: https://lightdock.org/tutorials/0.9.3/rna_docking

Execute the setup script for LightDock, specifying the protein and RNA PDB files. This command enables the calculation of normal modes (ANM) for both molecules.

```bash
lightdock3_setup.py protein.pdb rna.pdb -anm

```

--------------------------------

### Install LightDock

Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb

Installs the LightDock package and its dependencies. Ensure you are using version 0.9.0 as specified.

```bash
!pip install lightdock==0.9.0
```

```bash
!pip install pdb-tools
```

```bash
!pip install py3dmol
```

--------------------------------

### Setup LightDock for Membrane Simulation

Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb

Prepares the PDB files for LightDock simulation, specifying membrane environment and disabling certain options.

```bash
!lightdock3_setup.py 3x29_receptor_membrane.pdb 3x29_ligand.pdb --noxt --noh --membrane
```

--------------------------------

### Basic LightDock Simulation Execution

Source: https://lightdock.org/tutorials/0.9.3/basics

The simplest way to run a LightDock simulation, requiring only the setup file and the number of simulation steps.

```bash
lightdock3.py setup.json 10

```

--------------------------------

### Basic LightDock Setup Command

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

Executes the `lightdock3_setup.py` script with essential arguments for receptor and ligand PDB files, along with flags to exclude OXT atoms, hydrogens, waters, and enable ANM support.

```bash
lightdock3_setup.py 2UUY_rec.pdb 2UUY_lig.pdb --noxt --noh --now -anm
```

--------------------------------

### Verify LightDock Installation

Source: https://lightdock.org/tutorials/0.9.3/membrane

Check if LightDock is installed correctly by running the version command in the terminal.

```bash
lightdock3.py -v

```

--------------------------------

### Running a Basic LightDock Simulation

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

Executes a LightDock simulation with a specified setup file, number of steps, and number of CPU cores. This is a common command for initiating a docking process.

```bash
lightdock3.py setup.json 100 -c 1 -l 0
```

--------------------------------

### Execute the Simulation Script

Source: https://lightdock.org/tutorials/0.9.3/rust

Run the prepared execution script to start the lightdock-rust simulations. Ensure NUM_CORES is set appropriately in the script.

```bash
./execution.sh
```

--------------------------------

### Install LightDock via pip

Source: https://lightdock.org/tutorials/0.9.3/membrane

Install LightDock version 0.9.3.post1 using pip within a virtual environment. Ensure Python 3.6+ is used.

```bash
virtualenv venv
source venv/bin/activate
pip install lightdock==0.9.3.post1

```

--------------------------------

### Run LightDock3 Setup for 1CZY Complex

Source: https://lightdock.org/tutorials/0.9.3/rust

Execute the lightdock3_setup.py script to prepare the docking simulation for the 1CZY complex using the downloaded PDB and restraint files. This generates the necessary input for the lightdock-rust binary.

```bash
lightdock3_setup.py 1czy_protein.pdb 1czy_peptide.pdb --noxt --noh -anm -rst restraints.list -spr 10

```

--------------------------------

### Install LightDock in Jupyter/Colab

Source: https://lightdock.org/tutorials/0.9.3/membrane

Install LightDock version 0.9.3.post1 using pip in a Jupyter Notebook or Google Colab environment.

```python
!pip install lightdock==0.9.3.post1

```

--------------------------------

### GSO Configuration File Example

Source: https://lightdock.org/tutorials/0.9.3/basics

An example of a GlowWorm Swarm Optimization (GSO) configuration file, detailing parameters like rho, gamma, and initial Luciferin. Advanced users can modify these for custom simulations.

```ini
##
#
# GlowWorm configuration file - algorithm parameters
#
##

[GSO]

# Rho
rho = 0.4

# Gamma
gamma = 0.6

# Initial Luciferin
initialLuciferin = 5.0

# Initial glowworm vision range (in A)
initialVisionRange = 15.0

# Max vision range (in A)
maximumVisionRange = 40.0

# Beta
beta = 0.16

# Max number of neighbors
maximumNeighbors = 5

```

--------------------------------

### Example LightDock Output Line

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

An example line from a LightDock output file, detailing coordinates, IDs, scoring, and other parameters for a glowworm agent.

```text
#Coordinates  RecID  LigID  Luciferin  Neighbor's number  Vision Range  Scoring
( 8.3619938, -9.0568297, -23.0839562, -0.6368250, -0.1214085,  0.4488531, -0.6150161,  5.2922640,  4.6293871,  5.1679589,  3.6238049,  3.9717360,  7.2390017,  4.5821031,  5.4562578,  1.9734713,  2.9626742,  1.0323748,  5.8207747,  3.4377706,  2.6552282,  4.8705878,  3.0931470,  3.4670304,  3.9487060,  2.4948334,  4.5626560)    0    0  27.83190014  6 0.320  18.65982945

```

--------------------------------

### Run LightDock Simulation

Source: https://lightdock.org/tutorials/0.9.3/membrane

Execute the LightDock simulation using a setup file, specifying simulation steps, CPU cores, scoring function, and optionally a specific swarm to run.

```bash
lightdock3.py setup.json 100 -c 1 -s fastdfire -l 60

```

--------------------------------

### Run LightDock Simulation

Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb

Executes a LightDock simulation using a setup file, specifying swarm size, number of clusters, and search algorithm.

```bash
!lightdock3.py setup.json 100 -c 1 -s fastdfire -l 60 
```

--------------------------------

### Install PDB-Tools in Jupyter/Colab

Source: https://lightdock.org/tutorials/0.9.3/membrane

Install the PDB-Tools package using pip within a Jupyter Notebook or Google Colab environment.

```python
!pip install pdb-tools

```

--------------------------------

### Run Lightdock-Rust Simulation

Source: https://lightdock.org/tutorials/0.9.3/rust

Execute the lightdock-rust binary to simulate the first swarm. This command requires a setup JSON file, initial positions, number of steps, and a scoring function.

```bash
time ../../target/release/lightdock-rust setup.json init/initial_positions_0.dat 100 dfire
```

--------------------------------

### LightDock Model Generation Log

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

Example log output from the 'lgd_generate_conformations.py' script, showing the progress of reading PDB files and generating conformations.

```text
[generate_conformations] INFO: Reading ../lightdock_2UUY_rec.pdb receptor PDB file...
[generate_conformations] INFO: 1628 atoms, 223 residues read.
[generate_conformations] INFO: Reading ../lightdock_2UUY_lig.pdb ligand PDB file...
[generate_conformations] INFO: 415 atoms, 55 residues read.
[generate_conformations] INFO: Read 200 coordinate lines
[generate_conformations] INFO: Generated 200 conformations

```

--------------------------------

### View LightDock Output Header

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

Use the 'head' command to display the first few lines of a LightDock output file, showing the header and an example data line.

```bash
head -2 swarm_0/gso_100.out

```

--------------------------------

### Install PDB-Tools via pip

Source: https://lightdock.org/tutorials/0.9.3/membrane

Install the PDB-Tools package using pip. This package provides scripts for manipulating PDB files.

```bash
pip install pdb-tools

```

--------------------------------

### Command to Remove Generated Files

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

A utility command to clean up all files and directories generated by the LightDock setup process, useful for retrying the setup if it fails.

```bash
rm -rf lightdock* setup.json init/ swarm_*
```

--------------------------------

### LightDock Command-Line Usage

Source: https://lightdock.org/tutorials/0.9.3/basics

Displays the accepted command-line options when `lightdock3` is executed without arguments. This helps in understanding the available parameters for simulation setup.

```bash
usage: lightdock3 [-h] [-f configuration_file] [-s SCORING_FUNCTION] [-sg GSO_SEED] [-t TRANSLATION_STEP] 
                  [-r ROTATION_STEP] [-V] [-c CORES] [--profile] [-mpi] [-ns NMODES_STEP] [-min] [--listscoring]
                  [-l SWARM_LIST [SWARM_LIST ...]]
                  setup_file steps
lightdock3: error: the following arguments are required: setup_file, steps

```

--------------------------------

### Parallelize Lightdock Execution with ant_thony.py

Source: https://lightdock.org/tutorials/0.9.3/rust

This script automates the setup, data conversion, and execution of lightdock-rust simulations in parallel using ant_thony.py. Adjust NUM_CORES to match your system's CPU cores.

```bash
#!/bin/bash

# Edit only the number of cores to use for this simulation
NUM_CORES=4

# LightDock setup
lightdock3_setup.py 1czy_protein.pdb 1czy_peptide.pdb --noxt --noh -anm -rst restraints.list -spr 10

# Convert ANM data
lgd_flatten.py lightdock_rec.nm.npy rec_nm.npy
lgd_flatten.py lightdock_lig.nm.npy lig_nm.npy

# Calculate number of swarms
s=`ls -d swarm_* | wc -l`
swarms=$((s-1))

# Copy lightdock-rust binary
cp ../../target/release/lightdock-rust .

# Create a task.list file for ant_thony
for i in `seq 0 $swarms`;do echo "./lightdock-rust setup.json init/initial_positions_${i}.dat 100 dfire;" >> task.list; done

# Let ant_thony run
time ant_thony.py --cores ${NUM_CORES} task.list

# Clean task.list
rm -rf task.list

```

--------------------------------

### Visualize Swarm Centers with PyMOL

Source: https://lightdock.org/tutorials/0.9.3/membrane

This command visualizes the distribution of swarm centers over the receptor structure using PyMOL. It requires the receptor PDB file and the swarm centers file generated during setup.

```bash
pymol lightdock_3x29_receptor_membrane.pdb init/swarm_centers.pdb
```

--------------------------------

### Run Local RNA Docking Simulation

Source: https://lightdock.org/tutorials/0.9.3/rna_docking

Execute a local RNA docking simulation using LightDock. Specify the setup file, number of steps, scoring function, and number of CPU cores.

```bash
lightdock3.py setup.json 100 -s dna -c 8

```

--------------------------------

### DFIRE KeyError Example

Source: https://lightdock.org/tutorials/0.9.3/faq

This is an example of a KeyError that may occur with DFIRE scoring functions in older LightDock versions due to unrecognized atom types. It indicates that DFIRE does not recognize certain atom types, such as those in HETATM records or non-standard residues.

```python
File "/home/software/lightdock/lightdock/scoring/dfire/driver.py", line 152, in _get_docking_model
 anuma = atomnumber[rec_atom_type]
KeyError: 'LYSH1'

```

--------------------------------

### Download Data for 1CZY Complex Docking

Source: https://lightdock.org/tutorials/0.9.3/rust

Download necessary PDB and restraint files for performing a docking simulation on the 1CZY complex. These files are required for the setup process.

```bash
mkdir 1czy
cd 1czy
wget https://raw.githubusercontent.com/lightdock/lightdock-rust/master/example/1czy/1czy_protein.pdb
wget https://raw.githubusercontent.com/lightdock/lightdock-rust/master/example/1czy/1czy_peptide.pdb
wget https://raw.githubusercontent.com/lightdock/lightdock-rust/master/example/1czy/restraints.list

```

--------------------------------

### Example Residue Restraints

Source: https://lightdock.org/tutorials/0.9.3/dna_docking

This snippet shows the format of residue restraints within the 'restraints.list' file. It specifies restraints on the receptor (protein partner) at specific residues.

```text
R A.TRP.24
R A.VAL.26
R A.ARG.42
```

--------------------------------

### Download Residue Restraints List

Source: https://lightdock.org/tutorials/0.9.3/dna_docking

Download the predefined 'restraints.list' file, which specifies residue restraints to guide the docking process. This file is crucial for incorporating experimental or bioinformatic information.

```bash
curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/dna_docking/data/restraints.list
```

--------------------------------

### Generated setup.json Configuration

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

The `setup.json` file contains all parameters used for the LightDock simulation, useful for reproducibility and parameter verification. Avoid modifying this file unless you are certain of the implications.

```json
{
    "anm_lig": 10,
    "anm_rec": 10,
    "anm_seed": 324324,
    "flip": false,
    "glowworms": 200,
    "ligand_pdb": "2UUY_lig.pdb",
    "membrane": false,
    "noh": true,
    "now": true,
    "noxt": true,
    "receptor_pdb": "2UUY_rec.pdb",
    "restraints": null,
    "starting_points_seed": 324324,
    "surface_density": 50.0,
    "swarm_radius": 10.0,
    "swarms": 182,
    "transmembrane": false,
    "use_anm": true,
    "verbose_parser": false,
    "write_starting_positions": false
}
```

--------------------------------

### Set up LightDock Membrane Simulation

Source: https://lightdock.org/tutorials/0.9.3/membrane

Use this command to initialize a membrane simulation with specified receptor and ligand PDB files. Flags `--noxt` and `--noh` are used to ignore OXT and hydrogen atoms, respectively.

```bash
lightdock3_setup.py 3x29_receptor_membrane.pdb 3x29_ligand.pdb --noxt --noh --membrane
```

--------------------------------

### LightDock Simulation Command Help

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

Displays the usage information and available arguments for the `lightdock3` command. Use this to understand all possible simulation configurations.

```bash
usage: lightdock3 [-h] [-f configuration_file] [-s SCORING_FUNCTION] [-sg GSO_SEED] 
                  [-t TRANSLATION_STEP] [-r ROTATION_STEP] [-V] [-c CORES] [--profile] 
                  [-mpi] [-ns NMODES_STEP]
                  [-min] [--listscoring] [-l SWARM_LIST [SWARM_LIST ...]]
                  setup_file steps
lightdock3: error: the following arguments are required: setup_file, steps
```

--------------------------------

### Download Sample Data for 1AZP Complex

Source: https://lightdock.org/tutorials/0.9.3/dna_docking

Create a directory and download the necessary PDB files for the 1AZP protein-DNA complex. This is the initial step for setting up the docking simulation.

```bash
mkdir 1azp
cd 1azp
curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/dna_docking/data/1AZP_A.pdb
curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/dna_docking/data/1AZP_B.pdb
```

--------------------------------

### Download Sample Data for Docking

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

Use these commands to create a working directory and download the receptor and ligand PDB files required for the docking simulation.

```bash
mkdir test
cd test
curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/simple_docking/data/2UUY_rec.pdb
curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/simple_docking/data/2UUY_lig.pdb
```

--------------------------------

### Download Sample Data

Source: https://lightdock.org/tutorials/0.9.3/rna_docking

Create a directory and download the necessary PDB files for the 1A1T protein-RNA complex.

```bash
mkdir 1a1t
cd 1a1t
curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/rna_docking/data/1A1T_A.pdb
curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/rna_docking/data/1A1T_B.pdb

```

--------------------------------

### Open Receptor and Membrane in PyMOL

Source: https://lightdock.org/tutorials/0.9.3/membrane

Launch PyMOL with both the atomistic receptor PDB and the processed coarse-grained membrane PDB files to prepare for alignment.

```bash
pymol 3x29_receptor.pdb membrane_cg.pdb
```

--------------------------------

### Run Local Simulation with LightDock

Source: https://lightdock.org/tutorials/0.9.3/restraints

Execute a LightDock simulation on a local machine using specified parameters. This command simulates 55 swarms with 100 steps each, using the fastDFIRE scoring function and 8 CPU cores.

```bash
lightdock3.py setup.json 100 -s fastdfire -c 8

```

--------------------------------

### Compile LightDock-Rust from Source

Source: https://lightdock.org/tutorials/0.9.3/rust

Clone the repository and build the release version of the LightDock-Rust binary. The compiled executable will be located in the target/release directory.

```bash
git clone https://github.com/lightdock/lightdock-rust
cd lightdock-rust
cargo build --release

```

--------------------------------

### Simulate Single Swarm with LightDock

Source: https://lightdock.org/tutorials/0.9.3/restraints

Run a LightDock simulation for a specific swarm (ID=0) with limited resources. This command uses 1 core and simulates 100 steps for the first swarm.

```bash
lightdock3.py setup.json 100 -c 1 -l 0

```

--------------------------------

### Download Sample Data for Docking

Source: https://lightdock.org/tutorials/0.9.3/restraints

Use these curl commands to download the receptor and ligand PDB files for the 4G6M protein complex. Ensure you are in the correct directory before running.

```bash
mkdir test
cd test
curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/restraints/data/4G6M_rec.pdb
curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/restraints/data/4G6M_lig.pdb
```

--------------------------------

### Display LightDock Rust Command-Line Usage

Source: https://lightdock.org/tutorials/0.9.3/rust

Execute the lightdock-rust binary without arguments to display its usage instructions and required parameters.

```bash
./target/release/lightdock-rust 
Wrong command line. Usage: ./target/release/lightdock-rust setup_filename swarm_filename steps method

```

--------------------------------

### View Prediction Summary File

Source: https://lightdock.org/tutorials/0.9.3/rna_docking

Display the beginning of the 'solutions.list' file to inspect the summary of predicted structures, including swarm, glowworm, scores, and PDB file names.

```bash
head solutions.list
```

--------------------------------

### Protein Protonation with Reduce

Source: https://lightdock.org/tutorials/0.9.3/rna_docking

Prepare the protein PDB file by removing existing hydrogens and rebuilding them using the 'reduce' software for AMBER94 force-field compatibility.

```bash
reduce -Trim 1A1T_A.pdb > 1A1T_A_noh.pdb
reduce -BUILD 1A1T_A_noh.pdb > 1A1T_A_h.pdb

```

--------------------------------

### RNA Protonation with Reduce

Source: https://lightdock.org/tutorials/0.9.3/rna_docking

Prepare the RNA PDB file by removing existing hydrogens and rebuilding them using the 'reduce' software.

```bash
reduce -Trim 1A1T_B.pdb > 1A1T_B_noh.pdb
reduce -BUILD 1A1T_B_noh.pdb > 1A1T_B_h.pdb

```

--------------------------------

### Visualize Ligand PDB with py3Dmol

Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb

Loads and visualizes the ligand PDB file in a 3D viewer.

```python
import py3Dmol

with open("3x29_ligand.pdb") as ifile:
    ligand = "".join([x for x in ifile])

view = py3Dmol.view(width=600, height=600)
view.addModelsAsFrames(ligand)
view.setStyle({'model': -1}, {"cartoon": {'color': 'spectrum'}})
view.zoomTo()
view.show()
```

--------------------------------

### Generate Docking Conformations

Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb

Generates a specified number of conformations from the LightDock simulation output.

```bash
!lgd_generate_conformations.py 3x29_receptor_membrane.pdb 3x29_ligand.pdb swarm_60/gso_100.out 200
```

--------------------------------

### Generate Conformations with lgd_generate_conformations.py

Source: https://lightdock.org/tutorials/0.9.3/membrane

Generate predicted models from simulation output files. This script requires the receptor and ligand PDB files, the simulation output file, and the number of conformations to generate.

```bash
lgd_generate_conformations.py 3x29_receptor_membrane.pdb 3x29_ligand.pdb swarm_60/gso_100.out 200

```

--------------------------------

### HPC Post-processing PBS Script

Source: https://lightdock.org/tutorials/0.9.3/dna_docking

A comprehensive PBS script for post-processing LightDock simulation results on an HPC cluster. It includes steps for generating conformations, clustering, ranking, and filtering.

```bash
#PBS -N 1AZP-post
#PBS -q medium
#PBS -l nodes=1:ppn=8
#PBS -S /bin/bash
#PBS -d ./
#PBS -e ./postprocessing.err
#PBS -o ./postprocessing.out

### Calculate the number of swarms ###
s=`ls -d ./swarm_* | wc -l`
swarms=$((s-1))

### Create files for Ant-Thony ###
for i in $(seq 0 $swarms)
  do
    echo "cd swarm_${i}; lgd_generate_conformations.py ../protein.pdb ../dna.pdb  gso_100.out 200 > /dev/null 2> /dev/null;" >> generate_lightdock.list;
  done

for i in $(seq 0 $swarms)
  do
    echo "cd swarm_${i}; lgd_cluster_bsas.py gso_100.out > /dev/null 2> /dev/null;" >> cluster_lightdock.list;
  done

### Generate LightDock models ###
ant_thony.py -c 8 generate_lightdock.list;

### Clustering BSAS (rmsd) within swarm ###
ant_thony.py -c 8 cluster_lightdock.list;

### Generate ranking files for filtering ###
lgd_rank.py $s 100;

### Filtering models by >40% of satisfied restraints ###
lgd_filter_restraints.py --cutoff 5.0 --fnat 0.4 -lnuc rank_by_scoring.list restraints.list A B

```

--------------------------------

### Download Pre-formatted Restraint List

Source: https://lightdock.org/tutorials/0.9.3/restraints

Download a pre-formatted 'restraints.list' file using curl. This file contains residue restraints ready for use in LightDock.

```bash
curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/restraints/data/restraints.list
```

--------------------------------

### Full LightDock Analysis Protocol

Source: https://lightdock.org/tutorials/0.9.3/restraints

A comprehensive PBS script that automates the entire LightDock analysis workflow, including structure generation, intra-swarm clustering, ranking, and restraint-based filtering. It is designed for execution on an HPC cluster.

```bash
#PBS -N 4G6M-anal
#PBS -q medium
#PBS -l nodes=1:ppn=8
#PBS -S /bin/bash
#PBS -d ./
#PBS -e ./analysis.err
#PBS -o ./analysis.out

CORES=8

### Calculate the number of swarms ###
s=`ls -d ./swarm_* | wc -l`
swarms=$((s-1))

### Create files for Ant-Thony ###
for i in $(seq 0 $swarms)
  do
    echo "cd swarm_${i}; lgd_generate_conformations.py ../4G6M_rec.pdb ../4G6M_lig.pdb  gso_100.out 200 > /dev/null 2> /dev/null;" >> generate_lightdock.list;
  done

for i in $(seq 0 $swarms)
  do
    echo "cd swarm_${i}; lgd_cluster_bsas.py gso_100.out > /dev/null 2> /dev/null;" >> cluster_lightdock.list;
  done


### Generate LightDock models ###
ant_thony.py -c ${CORES} generate_lightdock.list;


### Clustering BSAS (rmsd) within swarm ###
ant_thony.py -c ${CORES} cluster_lightdock.list;


### Generate ranking files for filtering ###
lgd_rank.py $s 100;


### Filtering models by >40% of satisfied restraints ### 
lgd_filter_restraints.py --cutoff 5.0 --fnat 0.4 rank_by_scoring.list restraints.list A B > /dev/null 2> /dev/null;


```

--------------------------------

### Open Structures in PyMOL

Source: https://lightdock.org/tutorials/0.9.3/membrane

Opens the target docking model and the reference structure in PyMOL for visualization and analysis. Ensure both PDB files are in the current directory.

```bash
pymol swarm_22_112.pdb 3x29_reference.pdb

```

--------------------------------

### Generate Predicted Docked Models

Source: https://lightdock.org/tutorials/0.9.3/simple_docking

Use the 'lgd_generate_conformations.py' script to create PDB files for docked structures. Provide receptor, ligand, LightDock output, and the number of conformations to generate.

```bash
cd swarm_0
lgd_generate_conformations.py ../2UUY_rec.pdb ../2UUY_lig.pdb gso_100.out 200

```

--------------------------------

### Visualize Top Models with py3Dmol

Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb

Use this snippet to load a PDB file, add its models to a py3Dmol viewer, apply custom styles to chains and residues, and display the visualization. Ensure the PDB file exists at the specified path.

```python
import py3Dmol

with open("swarm_60/lightdock_115.pdb") as ifile:
    structure = "".join([x for x in ifile])

view = py3Dmol.view(width=600, height=600)
view.addModelsAsFrames(structure)
view.setStyle({'chain': 'A'}, {"cartoon": {'color': 'blue'}})
view.setStyle({'chain': 'B'}, {"cartoon": {'color': 'green'}})
view.setStyle({'resn':'MMB'}, {"sphere": {'color': 'orange'}})
view.zoomTo()
view.show()
```

--------------------------------

### Prepare Membrane PDB for LightDock

Source: https://lightdock.org/tutorials/0.9.3/membrane

Execute this Python script to parse, rename, and filter beads from a coarse-grained PDB file for membrane simulations in LightDock. Ensure the input PDB file is correctly named.

```bash
python3 prepare4lightdock.py 3x29_default_dppc-coarsegrained.pdb membrane_cg.pdb
```

--------------------------------

### Generate Predicted Models with lgd_generate_conformations.py

Source: https://lightdock.org/tutorials/0.9.3/basics

Use this command to generate PDB structure files for predicted models after a simulation. Ensure you provide the receptor structure, ligand structure, LightDock output file, and the number of glowworms.

```bash
usage: conformer_conformations [-h] [--setup setup_file]
                               receptor_structure ligand_structure lightdock_output glowworms
conformer_conformations: error: the following arguments are required: receptor_structure, ligand_structure, lightdock_output, glowworms
```

```bash
cd $LIGHTDOCK_HOME/examples/2UUY
cd swarm_0
lgd_generate_conformations.py ../2UUY_rec.pdb ../2UUY_lig.pdb gso_5.out 10
```

--------------------------------

### Cluster Docking Models

Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb

Clusters the generated docking models based on their Binding Site Similarity (BSS).

```bash
!lgd_cluster_bsas.py swarm_60/gso_100.out 
```

--------------------------------

### Generate LightDock PBS Script for HPC

Source: https://lightdock.org/tutorials/0.9.3/dna_docking

Create a PBS script to submit a LightDock job to an HPC cluster. This script defines job name, queue, resources, and the LightDock execution command.

```bash
#PBS -N LightDock-1AZP
#PBS -q medium
#PBS -l nodes=1:ppn=16
#PBS -S /bin/bash
#PBS -d ./
#PBS -e ./lightdock.err
#PBS -o ./lightdock.out

lightdock3.py setup.json 100 -s dna -c 16

```

--------------------------------

### Visualize Receptor PDB with py3Dmol

Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb

Loads and visualizes the receptor PDB file in a 3D viewer. Highlights membrane protein (MMB) with spheres.

```python
import py3Dmol

with open("3x29_receptor_membrane.pdb") as ifile:
    receptor = "".join([x for x in ifile])

view = py3Dmol.view(width=600, height=600)
view.addModelsAsFrames(receptor)
view.setStyle({'model': -1}, {"cartoon": {'color': 'spectrum'}})
view.setStyle({'resn':'MMB'}, {"sphere": {'color': 'orange'}})
view.zoomTo()
view.show()
```

--------------------------------

### Renumber Protein Atoms with PDB-Tools

Source: https://lightdock.org/tutorials/0.9.3/rna_docking

Renumber the atoms of the protein receptor partner using the PDB-Tools to ensure proper formatting for LightDock.

```bash
pdb_reatom 1A1T_A_h.pdb > protein.pdb

```

--------------------------------

### View Best Predicted Model in PyMOL

Source: https://lightdock.org/tutorials/0.9.3/membrane

Open the best predicted model from a swarm in PyMOL for visualization and analysis.

```bash
pymol swarm_60/lightdock_115.pdb

```

--------------------------------

### Extract Top Scoring Structures

Source: https://lightdock.org/tutorials/0.9.3/rna_docking

Use the 'get_top_structures.py' script to extract the top 10 scoring structures from the 'solutions.list' file. This creates a 'top_structures' directory with the best models.

```bash
./get_top_structures.py solutions.list
```

--------------------------------

### Clean Failed Simulation Directory

Source: https://lightdock.org/tutorials/0.9.3/faq

Use this command to remove all generated files from a failed LightDock simulation to ensure a clean restart. This prevents issues caused by partially generated files.

```bash
rm -rf lightdock_* init/ swarm_* setup.json *.npy top/ rank_by* solutions.list

```

--------------------------------

### PBS Script for RNA Docking Post-processing

Source: https://lightdock.org/tutorials/0.9.3/rna_docking

A PBS script to automate the generation of conformations, clustering, and ranking of RNA docking predictions. It calculates the number of swarms and uses Ant-Thony to parallelize tasks.

```bash
#PBS -N 1A1T-post
#PBS -q medium
#PBS -l nodes=1:ppn=8
#PBS -S /bin/bash
#PBS -d ./
#PBS -e ./postprocessing.err
#PBS -o ./postprocessing.out

### Calculate the number of swarms ###
s=`ls -d ./swarm_* | wc -l`
swarms=$((s-1))

### Create files for Ant-Thony ###
for i in $(seq 0 $swarms)
  do
    echo "cd swarm_${i}; lgd_generate_conformations.py ../protein.pdb ../rna.pdb  gso_100.out 200 > /dev/null 2> /dev/null;" >> generate_lightdock.list;
  done

for i in $(seq 0 $swarms)
  do
    echo "cd swarm_${i}; lgd_cluster_bsas.py gso_100.out > /dev/null 2> /dev/null;" >> cluster_lightdock.list;
  done

### Generate LightDock models ###
ant_thony.py -c 8 generate_lightdock.list;

### Clustering BSAS (rmsd) within swarm ###
ant_thony.py -c 8 cluster_lightdock.list;

### Generate ranking files ###
lgd_rank.py $s 100;
```

--------------------------------

### Make Execution Script Executable

Source: https://lightdock.org/tutorials/0.9.3/rust

Grant execute permissions to the execution script before running it. This is a standard step for shell scripts.

```bash
chmod u+x execution.sh
```

--------------------------------

### Submit RNA Docking Job to HPC Cluster

Source: https://lightdock.org/tutorials/0.9.3/rna_docking

Configure and submit an RNA docking simulation job to a High-Performance Computing (HPC) cluster using a PBS script. This script defines job parameters and execution commands.

```bash
#PBS -N LightDock-1A1T
#PBS -q medium
#PBS -l nodes=1:ppn=16
#PBS -S /bin/bash
#PBS -d ./
#PBS -e ./lightdock.err
#PBS -o ./lightdock.out

lightdock3.py setup.json 100 -s dna -c 16

```

--------------------------------

### Submit LightDock Job to HPC Cluster

Source: https://lightdock.org/tutorials/0.9.3/restraints

A PBS script to submit a LightDock simulation job to a High-Performance Computing cluster. It configures resources like nodes, cores, and specifies output/error file redirection.

```bash
#PBS -N LightDock-4G6M
#PBS -q medium
#PBS -l nodes=1:ppn=16
#PBS -S /bin/bash
#PBS -d ./
#PBS -e ./lightdock.err
#PBS -o ./lightdock.out

lightdock3.py setup.json 100 -s fastdfire -c 16

```

--------------------------------

### Perform Analysis

Source: https://lightdock.org/tutorials/0.9.3/rust

Execute the analysis script to process simulation results and generate the top 10 predicted poses. This script simplifies the post-simulation analysis.

```bash
./analysis.sh
```

--------------------------------

### Submit PBS Script

Source: https://lightdock.org/tutorials/0.9.3/restraints

Command to submit a PBS script to the Portable Batch System queue manager for execution on an HPC cluster.

```bash
qsub < submit_job.sh

```

--------------------------------

### Count Output Files

Source: https://lightdock.org/tutorials/0.9.3/rust

This command counts the number of generated GSO output files, which can be used to verify the completion of simulations.

```bash
find . -name gso_100.out | wc -l
```
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