ADCP 1.1 tutorials

Generate a rotamer library for a non-standard amino acid

This tutorial shows how to generate a rotamer library (.lib) file for a non-standard amino acid and use it in ADCP to dock peptides that contain it.

Step 1: get the example files

Download this zip file. It holds dummy non-standard amino acids and randomly generated Dunbrack-like rotamer files. Make a directory for the tutorial and unzip the file there:

mkdir -p ~/ADCP_examples/genLib
cd ~/ADCP_examples/genLib
wget https://github.com/sannerlab/downloads/releases/download/adcp-1.1/libGenExample.zip
unzip libGenExample.zip

The extracted input directory contains:

input/
├── libfiles
│   ├── FOO_random1.lib
│   └── SOO_random1.lib
├── pdbfiles
│   ├── D
│   │   ├── DFOO.pdb
│   │   └── DSOO.pdb
│   └── L
│       ├── FOO.pdb
│       └── SOO.pdb
└── rotamer_details.dat

Step 2: extract rotamer information

extractRotamerInfo -l input/libfiles/ -p input/pdbfiles/ -i _random1.lib -r input/rotamer_details.dat -o rotamerinfo.py

Output:

file 'rotamerinfo.py' is created successfully. Run 'makeLibFile' to generate lib file.

Step 3: generate the library file

makeLibFile -p input/pdbfiles -r input/rotamer_details.dat -t rotamerinfo.py -o my_foo_soo.lib

Output:

Using residue list from "input/rotamer_details.dat" for lib file generation!
Working on AA: FOO
Working on AA: SOO
Working on AA: DFOO
Working on AA: DSOO
ADCP acceptable lib file: 'my_foo_soo.lib' generated successfully

Step 4: dock with the new library

Download the example target file and run ADCP with the new library (-l):

mkdir trialRun
cd trialRun
wget https://github.com/sannerlab/downloads/releases/download/adcp-1.1/3Q47.trg
adcp -T 3Q47.trg -s "F<FOO>R<SOO>&F<FOO>&R<SOO>G" -w testDir -o myfoo -l ../my_foo_soo.lib -O -n 2000 -m 5

The peptide uses all four residues of the new library, followed by a glycine (ADCP needs more than 4 amino acids):

In the sequence Residue
F<FOO> FOO, with a phenylalanine bead in the coarse model
R<SOO> SOO, with an arginine bead
&F<FOO> D-FOO: the & makes it D, and ADCP takes its rotamers from DFOO in the library
&R<SOO> D-SOO, rotamers from DSOO
G glycine

The bead letters come from input/rotamer_details.dat (FOO F DFOO …, SOO R DSOO …). Write them in upper case: with a user rotamer library, a lower-case bead letter in front of a residue name makes the searches fail.

The run ends with a table of docked modes like this one; the values change from run to run:

mode |  affinity  | ref. | clust. | rmsd | energy | best |
     | (kcal/mol) | fnc  |  size  | stdv |  stdv  | run  |
-----+------------+------+--------+------+--------+------+
   1         -7.3      0.0       4      NA      NA    121
   2         -7.0      0.0       9      NA      NA    845
   3         -6.8      0.0      17      NA      NA    219
   4         -6.4      0.0       5      NA      NA    119
   5         -6.4      0.0       8      NA      NA    729

The docked poses are in testDir/myfoo_out.pdb, where residues 1 to 4 are named FOO, SOO, FOO and SOO.

Version 1.0 tutorials

The ADCP 1.0 tutorials (re-docking a linear peptide, re-docking a cyclic peptide) were written for the 1.0 command line. In 1.1 the target file option is -T instead of -t and the output files differ; see what changed in 1.1.

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