moldina-multiple-ligand-molecular-docking-over-autodock-vina

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moldina-multiple-ligand-molecular-docking-over-autodock-vina

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# Moldina

## Install

### Release installation

```
cd ./Moldina/build/linux/release/; make
```

### debug installation

```
cd ./Moldina/build/linux/debug/; make
```

### Inputs parameters

#### Input molecules (required) 
<pre>
  --receptor arg                        rigid part of the receptor (PDBQT) 
  --flex arg                            flexible side chains, if any (PDBQT) 
  --ligand arg                          ligand (PDBQT)
</pre>

#### Search space (required)
<pre>
  --center_x arg                        X coordinate of the center 
  --center_y arg                        Y coordinate of the center 
  --center_z arg                        Z coordinate of the center 
  --size_x arg                          size in the X dimension (Angstroms) 
  --size_y arg                          size in the Y dimension (Angstroms) 
  --size_z arg                          size in the Z dimension (Angstroms)
</pre>

#### Output (optional)
<pre>
  --out arg                             output models (PDBQT), the default is chosen based on the ligand file name
  --log arg                             optionally, write log file
</pre>

#### Advanced options (see the manual)
<pre>
  --score_only                          score only - search space can be omitted 
  --local_only                          do local search only 
  --randomize_only                      randomize input, attempting to avoid clashes 
  --search_alg_PSO                      if true, uses particle swarm optimization as main optimizing algorithm 
  --ligands arg                         list of ligands to dock for simulataneous docking 
  --population arg (=500)               population size for particle swarm optimization (minimum 5) 
  --weight_gauss1 arg (=-0.035579)      gauss_1 weight 
  --weight_gauss2 arg (=-0.005156)      gauss_2 weight 
  --weight_repulsion arg (=0.84024500000000002) 
                                        repulsion weight
  --weight_hydrophobic arg (=-0.035069000000000003)
                                        hydrophobic weight
  --weight_hydrogen arg (=-0.58743900000000004)
                                        Hydrogen bond weight
  --weight_rot arg (=0.058459999999999998) 
                                        N_rot weight 
</pre>

#### Misc (optional)
<pre>
  --cpu arg                             the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)  
  --seed arg                            explicit random seed 
  --exhaustiveness arg (=8)             exhaustiveness of the global search (roughly proportional to time): 1+ 
  --num_modes arg (=9)                  maximum number of binding modes to generate 
  --energy_range arg (=3)               maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) 
</pre>

#### Configuration file (optional)
<pre>
  --config arg                          the above options can be put here
</pre>

#### Information (optional)
<pre>
  --help                                display usage summary 
  --help_advanced                       display usage summary with advanced options 
  --version                             display program version
</pre>

### Docking example

#### 1s63

```
./Moldina --config config_1s63.txt --cpu 1 --population 50
```

##### Config file

<pre>
receptor = 1s63/1s63_prot.pdbqt
center_x = 19.371
center_y = 131.729
center_z = -1.475
size_x = 30
size_y = 30
size_z = 30
energy_range = 100
num_modes = 15
search_alg_PSO = 1
ligands = 1s63/ligs.txt
</pre>

#### 5x72

```
./Moldina --config config_5x72.txt --cpu 1 --population 50
```

##### Config file

<pre>
receptor = 5x72/5x72_prot.pdbqt
center_x = -15.64
center_y = 16.044
center_z = 129.498
size_x = 20
size_y = 20
size_z = 20
energy_range = 100
num_modes = 15
search_alg_PSO = 1
ligands = 5x72/ligs.txt
</pre>

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