SPOT-1D-LM

SPOT-1D-LM: Reaching Alignment-profile-based Accuracy in Predicting Protein Secondary and Tertiary Structural Properties without Alignment.

System Requirements

Hardware Requirements: SPOT-1D-LM predictor has been tested on standard ubuntu 18 computer with approximately 32 GB RAM to support the in-memory operations.

• Python3.7
• Anaconda
• CUDA 10.1 (Optional if using GPU)
• cuDNN (>= 7.4.1) (Optional if using GPU)

Installation

To install SPOT-1D-LM and it's dependencies following commands can be used in terminal:

1. git clone https://github.com/jas-preet/SPOT-1D-LM.git
2. cd SPOT-1D-LM

To download the model check points from the dropbox use the following commands in the terminal:

3. wget https://apisz.sparks-lab.org:8443/downloads/Resource/Protein/2_Protein_local_structure_prediction/SPOT-LM-checkpoints.xz
4. tar -xvf SPOT-LM-checkpoints.xz

To install the dependencies and create a conda environment use the following commands

5. conda create -n spot_1d_lm python=3.7
6. conda activate spot_1d_lm

if GPU computer: 7. conda install pytorch==1.7.0 torchvision==0.7.0 cudatoolkit=10.1 -c pytorch

for CPU only 7. conda install pytorch==1.6.0 torchvision==0.7.0 cpuonly -c pytorch

8. pip install fair-esm

9. conda install pandas=1.1.1

10. conda install tqdm

11. pip install bio-embeddings[all]

Execute

To run SPOT-1D-LM use the following command

bash run_SPOT-1D-LM.sh file_lists/test_file_list.txt cpu cpu cpu to run model, ESM-1b and ProtTrans on cpu

or

bash run_SPOT-1D-LM.sh file_lists/test_file_list.txt cpu cpu cuda:0 to run model on gpu and, ESM-1b and ProtTrans on cpu

or

bash run_SPOT-1D-LM.sh file_lists/test_file_list.txt cuda:0 cuda:1 cuda:2 to run model, ESM-1b and ProtTrans on gpu

Citation Guide

for more details on this work refer the manuscript

Please also cite and refer to ESM-1b and ProtTrans as the input used in this work is from these works.