dongcf / absolut

Unconstrained lattice antibody-antigen bindings generator

Absolut!

Unconstrained lattice antibody-antigen bindings generator - One tool to simulate them all!

Absolut! allows the user to generate custom datasets by discretizing new antigens or annotating custom CDRH3 sequences enabling the on-demand generation of large synthetic datasets for 3D-antibody-antigen binding generated under the same, deterministic settings, with accessible computing resources.

A Greifflab product! Contact for issues / questions: philippe dot robert at ens minus lyon dot org

Please inform us with the above e-mail when creating an issue request in this github, we do not get automatic notification.

Absolut! software

• takes PDB antigens, converts them into lattice representation with integer positions.
• takes CDR3 Amino Acid sequences, and computes their best binding around a lattice antigen.
• generates features of antibody-antigen bindings directly usable for Machine Learning

Absolut! database

The database generated with Absolut! is available as repository in NIRD research data storage. The files can directly be accessed by http Database Files.

Documentation / Reference / Reproducing

You can find a more detailed documentation in the subfolder doc/HowToAbsolut.pdf

The method and analyses of antibody-antigen bindings are explained in:

• Robert and Akbar et al. 2021, Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for real-world antibody specificity prediction', BioRXiV link
• Robert et al 2020, 'Ymir: A 3D structural affinity model for multi-epitope vaccine simulations', iScience link

It has been used to benchmark antibody generative ML models in: Akbar and Robert et al 2021 mAbs, 'In silico proof of principle of machine learning-based antibody design at unconstrained scale' link

The scripts to reproduce Robert et al. 2021 are also provided in this repository in the folder scripts/ link

License: https://github.com/csi-greifflab/Absolut/blob/main/20221122%20Absolutt%20license.pdf

Download / clone

git clone https://github.com/csi-greifflab/Absolut

Usage

Absolut! can be compiled into three versions: one that doesn't require any library to be installed (AbsolutNoLib), the full version (Absolut), and a version specific for using MPI (AbominationMPI). See Installation for details.

Calling Absolut alone shows the list of available options.

./Absolut 
#or
./AbsolutNoLib

An all-in-one example for most tasks is:
plan 3GB of disk space, 2 GB memory and 500MB download

#With ./Absolut or ./AbsolutNoLib:

# Get the list of available lattice antigens
./AbsolutNoLib listAntigens

# Get the sequence and surface residue of each antigen
./AbsolutNoLib info_antigens

# Get the full information on a particular antigen
./AbsolutNoLib info_antigen 1ADQ_A

# Get the list of precomputed CDRH3 possible structures for an antigen
./AbsolutNoLib info_filenames 1FBI_X
wget http://philippe-robert.com/Absolut/Structures/SULSU040643e2c0a6d6343bbe8a27b079ef91-10-11-efc862c2cdef086ba79606103a3dfc62Structures.txt

# Get the antibody-antigen complex of a CDRH3 sequence to an antigen (requires the downloaded file above to be in the same folder)
./AbsolutNoLib singleBinding 1FBI_X CARAAHKLARIPK

# High throughput calculation of antibody-antigen complexes for a list (repertoire) of CDRH3 sequences. Here, requests 10 threads in parallel.
./AbsolutNoLib repertoire 1FBI_X SmallSetCDR3.txt 10  #SmallSetCDR3.txt is a provided example list of CDR3s inside src/

# Calculation of structure and sequence encodings from the produced list of antibody-antigen complexes
./AbsolutNoLib getFeatures 1FBI_X 1FBI_XFinalBindings_Process_1_Of_1.txt outputFeaturesFile.txt 1 true

# Generating new antigens and visualizing complexes is only possible with the full ./Absolut

# Takes a PDB and the chains of interests, lattice resolution and discretization method and returns the C++ code for the antigen [New antigens would need to be manually added to antigenLib.cpp].
./Absolut discretize 1CZ8 VW 5.25 FuC

# Visualizing of available antigens in 3D
./Absolut visualize 1FBI_X 

# Visualizing many binding complexes  
./Absolut visualize 1FBI_X 1FBI_XFinalBindings_Process_1_Of_1.txt -95.5

# Visualizing binding hotspots
./Absolut hotspots 1FBI_X 1FBI_XFinalBindings_Process_1_Of_1.txt -95.5 4 

Installation

Absolut! was written in C++.

Three versions are provided with more or less library requirements: Absolut, AbsolutNoLib and AbominationMPI. All versions require a C++ compiler. We recommend starting with AbsolutNoLib, which is easier to install, as most tasks are already available with this version.

1/ AbsolutNoLib requires no additional library, and can perform all tasks except user interface for discretization and 3D visualization. We recommend first compiling/running AbsolutNoLib, which should work smoothly.

# Make sure to have a g++ compiler and make, for instance sudo apt-get install build-essential 
cd src
make		# This creates 'AbsolutNoLib' executable. 

2/ AbominationMPI is the MPI parallelized version for high throughput repertoire bindings generation.

• requires MPI compiler and headers

cd src
#Depending on your MPI compiler,
make MPIcxx
#or
make MPIc++
#or
make MPIgxx
# This creates 'AbominationMPI' executable.

3/ Absolut is the full version,

• requires the Qt framework
• requires freeglut library (or another other C++ glut library) for visualizing 3D lattice structures
• requires the gsl library for discretizing new antigens
• requires wget and curl, for downloading files (like PDBs when discretizing)
• optionally, a sorftware to visualize PDBs (like rasmol)

Installing and then linking the libraries can be tricky depending on the OS. Full help for installing these libraries (especially in Windows) is provided in the documentation doc/HowToAbsolut It is also possible to use Absolut! with a user-defined custom subset of libraries (See in the full documentation).

Installing on linux (simplest):

#sudo apt-get install build-essential  #if you don't have g++ and make 
sudo apt-get install libgsl-dev
sudo apt-get install curl
sudo apt-get install libgsl-dev
sudo apt-get install freeglut3-dev

#to find the available qt packages in your distribution
apt-cache search qtbase
apt-cache search libqt5

#These packages should do the job
sudo apt-get install qtbase5-dev
sudo apt-get install qtcreator
sudo apt-get install libqt5svg5
sudo apt-get install libqt5printsupport5

#To visualize PDB structures during discretization
sudo apt-get install rasmol

#For using pdb-tools (manipulating pdb files during discretization), python is needed
# sudo apt install python3
# and make sure that python is callable by "python":
sudo apt-get install python-is-python3

Installing on Windows:

Compiling

#Please DO NOT compile the full version in src/ folder, it would destroy the Absolut/ subfolder and the original Makefile ...
#We recommend to compile into src/bin because Absolut! expects the pdb-tools scripts to be directly in ../pdb-tools
cd src/bin/
qmake ../Absolut/Absolut.pro	#qmake creates a new Makefile embedding Qt libraries locations
make		#This creates Absolut

Alternately, if you have installed the Qt framework with qtcreator,

qtcreator Absolut/Absolut.pro
#or
qtcreator Absolut/AbsolutNoLib.pro
#or
qtcreator Absolut/AbsolutNoLibMPI.pro

Installing on MAC:

#if no recent g++ compiler, use this command (will also install g++)
brew install gcc 
brew install wget
brew install qt
brew install gsl
brew install freeglut

Then, from the src/bin/ folder,

qmake ../Absolut/Absolut.pro
make

Some OS specific points: Inside Absolut/Absolut.pro, your compiler might recognize only -o1 or -O1. Linking the libraries might require that you provide their folder. Can either add it in the Absolut.pro linker options, or inside the Makefile manually (but then do not run qmake anymore). -framework openGL should work for openGL and already be added. Depending on your g++ compiler, there might be conflicts between the C++ language of the libraries and the C++ standard libraries provided with the compiler. This might be solved by adding "QMAKE_CXXFLAGS += -std=c++14 -std=c++17" inside Absolut/Absolut.pro. We didn't add these lines by default in case your C++ compiler doesn't support C++17.

Note, the libraries Latfit, pdb-tools and soil are provided inside Absolut with their compatible version (and do not need to be installed by the user) - Latfit has been slighty modified to consider the center of a full residue (not only the side-chain) during discretization

AbsolutNoLib has been run on a HPC cluster with CentOS Linux version 7, and gcc version 4.8.5 (no other libraries required). The full Absolut! has been run on windows 10, using gcc 7.3.0 (MinGW-W64), gsl 2.6, GNU Wget 1.11.4, Qmake 3.1, Qt version 5.12.5 and freeglut 3.2.1

Step-by-step use cases

Discretization of antigens WITHOUT user interface

./Absolut discretize 1CZ8 VW 5.25 FuC

Inputs

• PDB_ID: The 4-character name of the PDB to discretize (will automatically download if not in the folder)
• Chains: The names of the chains to be discretized (one char per chain, put together)
• Resolution: The resolution of the 3D lattice [default 5.25]
• TypePos The: type of positions used for discretization [CA for Carbon Alpha, CoM for Centroid center of the side-chain only, and FuC for fused center of the whole AA – default FuC]

Outputs

• PDB and fasta files: are downloaded from the PDB server
• 1CZ8deIns.pdb: PDB with removed insertions (using pdb-tools)
• 1CZ8_VWprepared.pdb: new PDB with only the chains of interest
• 1CZ8discretized5.25FuC.pdb: discretized chains outputed from LatFit
• 1CZ8_VWInLattice.txt: Description of the discretized (lattice) antigen [Each chain is described as a starting position in the lattice (6-digits number) and a list of moves in space (straight S, up U, down D, left L, right R). See ‘info_position’ to convert lattice positions.

Discretization of antigens WITH user interface

./Absolut discretize

The inputs are decided from the user interface (and can also be provided in the command line). Identical outputs as above. Possible to export pictures during visualization inside the interface (command 'O', see documentation on visualization).

Get the list of available lattice antigens

./Absolut listAntigens

Output

0	1FNS_A
1	1ADQ_A
2	1FSK_A
3	1FBI_X
4	1H0D_C

The library of lattice antigens is defined inside antigenLib.cpp. Their name is "PDB_Chains", for instance "1CZ8_VW". More than 150 lattice antigens are already available. If you wish to add your own, please manually add them into antigenLib.cpp.

Generation of a bindings of CDR3s on a lattice (discretized) antigen from the library

This takes a lattice antigen and a list of CDR3s sequences and returns the best binding structure of each 11-mers of each CDR3 around the antigen.

There are two ways. The singleBinding option allows to calculate for one CDR3 in particular and is good for testing. The repertoire option allows to process a text file with a list of CDR3s.

Step 1: Get requested pre-computed files (once only)

./Absolut info_fileNames 1FBI_X
wget ...

Output

Pre-calculated structures are in SULSU040643e2c0a6d6343bbe8a27b079ef91-10-11-efc862c2cdef086ba79606103a3dfc62Structures.txt
use:
wget http://philippe-robert.com/Absolut/Structures/SULSU040643e2c0a6d6343bbe8a27b079ef91-10-11-efc862c2cdef086ba79606103a3dfc62Structures.txt

Step 2: Calculate the bindings, after the precomputed structure file is in the same (or parent) folder

#For one CDR3 only
./Absolut singleBinding 1FBI_X CARAAHKLARIPK

#For a list of CDR3s provided in ListCDR3s.txt
./Absolut repertoire 1FBI_X ListCDR3s.txt

#Or, without MPI, the program is still paralellized to use multiple threads, for instance 20 here
./Absolut repertoire 1FBI_X ListCDR3s.txt 20

#Or, in order to use MPI, for instance using 50 threads for each MPI process
mpiexec –n NbProcesses ./AbominationMPI repertoire 1FBI_X ListCDR3s.txt 50

Inputs

• Antigen_ID: The ID of the antigen in the library.
• ListCDR3s.txt: a text file with a list of CDR3s. Two columns, ID and CDR3 Amino Acid sequence, tab-separated, no header:

1	CAGPSTTVPYYFDYW
2	CARAYYSNDYW
3	CARWDDYDDWFAYW
4	CARESSGYGYW
5	CARYNYGPMDYW
6	CARGDSFDYW
7	CARVPNWDVNWSFDVW
...

Note, only the CDR3s with 11 AAs or more will be considered.

• A precomputed structure file in the folder (or parent folder) where Absolut is called. This is a text file containing the list of all pre-calculated prossible bindings. You can use the wget command provided when calling ./Absolut info_fileNames. We have precalculated these files for the library antigens and made them available in http://philippe-robert.com/Absolut/Structures/ Note, it is possible to recompute the structure files for a library antigen or any new home-made antigens, by using the command singleBinding above, that will regenerate the files if not present in the folder. The repertoire option stops if the files are not available.

Outputs

• Text file called "1FBI_XFinalBindings_Process_1_Of_1.txt", containing the structural annotation on how each 11-mer (Slide) binds to the antigen, with its binding energy and its structure (position-list of moves) A new ID is generated for each slide, with the CDR3ID from the input file followed with _ and the number of the slide and a/b/c... if different structures share the best binding energy. The best way a CDR3 binds to the antigen is annotated with Best=true. This file format is called Raw Binding dataset

#Antigen 1FBI
ID_slide_Variant      CDR3		Best	Slide	Energy	Structure
42881_00a	CARDIVTTWPYYAMDYW	false	CARDIVTTWPY	-54.77	129120-DSLLRRDDSD
42881_01a	CARDIVTTWPYYAMDYW	false	ARDIVTTWPYY	-61.49	125152-UUUSURUDUD
42881_02a	CARDIVTTWPYYAMDYW	false	RDIVTTWPYYA	-54.07	141278-SLSSRRSDDS
42881_03a	CARDIVTTWPYYAMDYW	false	DIVTTWPYYAM	-59.4	121119-RUSLLSDDUD
42881_03b	CARDIVTTWPYYAMDYW	false	DIVTTWPYYAM	-59.4	116959-USSDDSRRLR
42881_04a	CARDIVTTWPYYAMDYW	false	IVTTWPYYAMD	-62.9	121055-USDDSRRLRL
42881_05a	CARDIVTTWPYYAMDYW	false	VTTWPYYAMDY	-64.95	137374-URDSRUURDU
42881_06a	CARDIVTTWPYYAMDYW	true	TTWPYYAMDYW	-65.09	141405-SSSDRRDLRS
42882_00a	CARDKGAYSNSWYFDVW	false	CARDKGAYSNS	-47.55	137312-RULUUSUSDS
42882_01a	CARDKGAYSNSWYFDVW	true	ARDKGAYSNSW	-48.6	129120-DSLSDLSLLD
…

Analyze the 3D binding features from a raw binding

./Absolut getFeatures 1FBI_X 1FBI_XRawBindings.txt outputFeaturesFile.txt
#or, it is possible to precise the binding degree in the analysis by adding the degree (1 here) and true/false to include the degree into the encodings
./Absolut getFeatures 1FBI_X 1FBI_XRawBindings.txt outputFeaturesFile.txt 1 true

Inputs

• Antigen ID
• 1FBI_XRawBindings.txt: The raw binding file generated from the repertoire option below
• outputFeaturesFile.txt: The file that will be created with the binding features
• degree(optional): this specify that only AA interactions of degree equal or more than X (between antibody and antigen) are taken into the encoding
• showDegreeInAnalyses: this will add the degree into the coarse grained encodings, like the motif XX-X-X will become X1X2--X1--X3.

Outputs

• outputFeaturesFile.txt with the same lines as the input line, but extended with one column per feature. The features are:

Note: you might want to keep only the best Slides per CDR3 (Best=true) from the raw binding file before generating the features.

Visualize antigens and bindings in 3D (Needs full Absolut! version)

To visualize an antigen from the library

./Absolut visualize 1FBI_X

To include the bindings from a raw binding with an optional energy threshold

./Absolut visualize 1FBI_X 1FBI_XRawBindings.txt
./Absolut visualize 1FBI_X 1FBI_XRawBindings.txt -95.5

Generate binding hotspots from a raw binding

./Absolut hotspots 1FBI_X 1FBI_XRawBindings.txt -95.5

User-requested additions <only usable with the full Absoltut, but does not start or need the GUI>:

It is now possible to perform the antigen discretization step by step from command line:

Selecting the chain and removing insertions

./Absolut discretize_delete_insertions 1ADQ A 
output: 1ADQdeIns.pdb

Using latfit to generate a discretized PDB

./Absolut discretize_latfit_to_discrete_pdb  1ADQ  A  1ADQdeIns.pdb
output: 1ADQ_AdiscretizedFuC5.25.pdb

or with non-default parameters:

./Absolut discretize_latfit_to_discrete_pdb  1ADQ  A  1ADQdeIns.pdb 6 CoM false 40
output: 1ADQ_AdiscretizedCoM6.pdb

Last step, from the latfit output to the inLattice text file

./Absolut discretize_discrete_pdb_to_lattice 1ADQ A 1ADQ_AdiscretizedFuC5.25.pdb 
output: 1ADQ_Ainlattice.txt