Repository for publicly available deep learning models developed in Rosetta community

Related tags

Deep Learning trRosetta2
Overview

trRosetta2

This package contains deep learning models and related scripts used by Baker group in CASP14.

Installation

Linux/Mac

  1. clone the package
git clone https://github.com/RosettaCommons/trRosetta2
cd trRosetta2
  1. create conda environment using one of the .yml files: casp14-baker-linux-cpu.yml, casp14-baker-linux-gpu.yml, casp14-baker-mac-cpu.yml
conda env create -f casp14-baker-linux-gpu.yml
conda activate casp14-baker
  1. download network weights [1.1G]
wget https://files.ipd.uw.edu/pub/trRosetta2/weights.tar.bz2
tar xf weights.tar.bz2
  1. download and install third-party software
./install_dependencies.sh
  1. download sequence and structure databases
# uniclust30 [46G]
wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz
mkdir -p UniRef30_2020_06
tar xf UniRef30_2020_06_hhsuite.tar.gz -C ./UniRef30_2020_06

# structure templates [8.3G]
wget https://files.ipd.uw.edu/pub/trRosetta2/pdb100_2020Mar11.tar.gz
tar xf pdb100_2020Mar11.tar.gz

Obtain a PyRosetta licence and install the package in the newly created casp14-baker conda environment (link).

Usage

mkdir -p examples/T1078
./run_pipeline.sh example/T1078.fa example/T1078

Links

References

[1] I Anishchenko, M Baek, H Park, J Dauparas, N Hiranuma, S Mansoor, I Humphrey, D Baker. Protein structure prediction guided by predicted inter-residue geometries. In: CASP14 Abstract Book, 2020

[2] H Park, M Baek, N Hiranuma, I Anishchenko, S Mansoor, J Dauparas, D Baker. Model refinement guided by an interplay between Deep-learning and Rosetta. In: CASP14 Abstract Book, 2020

[3] M Baek, I Anishchenko, H Park, I Humphrey, D Baker. Protein oligomer structure predictions guided by predicted inter-chain contacts. In: CASP14 Abstract Book, 2020

Comments
  • Adding Benchmark scripts and outline for run-pipeline.py

    Adding Benchmark scripts and outline for run-pipeline.py

    @gjoni @minkbaek this pull request is a follow up to our last meeting. It adds:

    • outline for run-pipeline.py (ie Python rewrite of run_pipeline.sh script)
    • add script to install dependencies (part of run-pipeline.py script now)
    • add scripts needed for Benchmark integration
    opened by lyskov 2
  • T1078 example couldn't get the model file

    T1078 example couldn't get the model file

    Thank you very much for the release of this software, this work is significant for biological research. After the installation is complete, I follow the instructions to run the sample code. It shows： bash run_pipeline.sh example/T1078.fa example/T1078 Running hhsearch Running trRefine /home/rrrna/trRosetta2 Picking final models Final models saved in: example/T1078/model The program generates a lot of files in the T1078 folder, but there is no file in model/. T1078$ ls DONE_iter0 log pdb-msa t000_.msa0.a3m t000_.ss2 DONE_iter1 model pdb-tbm t000_.msa0.ss2.a3m t000_.tape.npy hhblits parallel.list pdb-trRefine t000_.msa.npz trRefine_fold.list

    opened by mooerccx 1
  • Does the

    Does the "run_pipeline.sh" script ignore "Run modeling w/ trRefine output" part automatically?

    The "Run trRefine" part creates a file named DONE_iter1 which make "! -f $WDIR/DONE_iter1" false.

    ############################################################
# 7. Run trRefine
############################################################
if [ ! -s $WDIR/t000_.trRefine.npz ]
then
    echo "Running trRefine"
    cd $WDIR
    python $PIPEDIR/trRefine/run_trRefine_DAN.py -msa_npz $WDIR/t000_.msa.npz \
        -tbm_npz $WDIR/t000_.tbm.npz -pdb_dir_s $WDIR/pdb-msa $WDIR/pdb-tbm \
        -a3m_fn $WDIR/t000_.msa0.a3m -hhr_fn $WDIR/t000_.hhr\
        -n_core $CPU > $WDIR/log/trRefine.stdout 2> $WDIR/log/trRefine.stderr
    cd ..
    touch $WDIR/DONE_iter1
fi


############################################################
# 8. Run modeling w/ trRefine output
############################################################

if [ ! -f $WDIR/DONE_iter1 ]
    opened by EstherBear 1
  • json.decoder issue

    json.decoder issue

    Generating TAPE features 243B [00:00, 284458.80B/s] Traceback (most recent call last): File "/home/ngayatri/trRosetta2/trRosetta2/tape/get_embeddings.py", line 25, in model = ProteinBertModel.from_pretrained('bert-base') File "/home/ngayatri/miniconda3/envs/casp14-baker/lib/python3.6/site-packages/tape/models/modeling_utils.py", line 470, in from_pretrained *kwargs File "/home/ngayatri/miniconda3/envs/casp14-baker/lib/python3.6/site-packages/tape/models/modeling_utils.py", line 172, in from_pretrained config = cls.from_json_file(resolved_config_file) File "/home/ngayatri/miniconda3/envs/casp14-baker/lib/python3.6/site-packages/tape/models/modeling_utils.py", line 202, in from_json_file return cls.from_dict(json.loads(text)) File "/home/ngayatri/miniconda3/envs/casp14-baker/lib/python3.6/json/init.py", line 354, in loads return _default_decoder.decode(s) File "/home/ngayatri/miniconda3/envs/casp14-baker/lib/python3.6/json/decoder.py", line 339, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/home/ngayatri/miniconda3/envs/casp14-baker/lib/python3.6/json/decoder.py", line 357, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) Running sequence-based trRosetta Folding trRosetta models Running trRefine /home/ngayatri/trRosetta2/trRosetta2 Folding trRefine models ls: cannot access /home/ngayatri/trRosetta2/trRosetta2/example/T1078/pdb-trRefine/model.pdb: No such file or directory Running DeepAccNet-msa on trRefine models

    please help me solve this issue

    opened by GayatriNavle 4
  • Pick final model not works

    Pick final model not works

    I tried TrRosetta2 on 1crn fasta. I had to recompile hhsuite to avoid segmentation fault issue.

    All the pipeline look works fine but at the end final_pick.py fail because it not found _acc file in pdb-TrRefine.

    I would like to ask help to fix this issue.

    opened by luigidibiasi 0
  • Error while running trRosetta2

    Error while running trRosetta2

    Hi, I get this error while running the pipeline script. No PDB model is generated. Could you please help me out with this ?

    Traceback (most recent call last): File "./get_embeddings.py", line 25, in model = ProteinBertModel.from_pretrained('bert-base') File "/mnt/NewHDD/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tape/models/modeling_utils.py", line 470, in from_pretrained **kwargs File "/mnt/NewHDD/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tape/models/modeling_utils.py", line 172, in from_pretrained config = cls.from_json_file(resolved_config_file) File "/mnt/NewHDD/anaconda3/envs/casp14-baker/lib/python3.6/site-packages/tape/models/modeling_utils.py", line 202, in from_json_file return cls.from_dict(json.loads(text)) File "/mnt/NewHDD/anaconda3/envs/casp14-baker/lib/python3.6/json/init.py", line 354, in loads return _default_decoder.decode(s) File "/mnt/NewHDD/anaconda3/envs/casp14-baker/lib/python3.6/json/decoder.py", line 339, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/mnt/NewHDD/anaconda3/envs/casp14-baker/lib/python3.6/json/decoder.py", line 357, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

    Best,

    Anupam

    opened by anu-bioinfo 5
  • How to fold and dock for homodimer and heterodimer

    How to fold and dock for homodimer and heterodimer

    Hi,

    Thanks for sharing this tool. And the run_pipeline.sh is just for monomer structure prediction, right? Could you also share the whole pipeline scripts for the homo- and hetero-structure prediction. Thanks in advance.

    opened by ZhiYeG 0
  • Error message running Tape about undefined symbol omp_get_num_procs

    Error message running Tape about undefined symbol omp_get_num_procs

    Error message running Tape about undefined symbol omp_get_num_procs Resolved using conda install --channel conda-forge llvm-openmp

    https://github.com/ContinuumIO/anaconda-issues/issues/10195

    opened by FrBonnardel 0
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