PUNCH2

A residue-level Intrinsically Disordered Region/Protein(IDP/IDR) predictor trained on PDB and Disprot Databases.

📝 Description

PUNCH2 project belongs to a serious of PUNCH projects which focus on the Structure and Function prediction of Intrisically Diordered Protein/Region (IDP/IDR). Currently we have PUNCH2 for IDR structure prediction, and PUNCH_Linker and PUNCH_Linker_Light for DFL prediction.

🐣 Getting Started

Currently, we provide two ways to use this perdictor: Docker or Download source code from this Github.

Pre-requirements

This predictor requires sequences embedded with ONEHOT, ProtTrans, and MSA Transformer.

Note,

• File format should be [SEQUENCE_NAME/ID].npy, replace SEQUENCE_NAME/ID with the actural sequence ID, it should be the same as the name from .fasta file.
• Matrix shape:
  Onehot: (1, 227, 21)
  ProtTrans: (1, 227, 1024)
  MSA Transformer: (1, 227, 768)

📣‼️If you don't have them available, please visit the embedding section of our project first to embed the sequences.‼️

(We maintain this separation due to the requirements from CAID3, but we may edit or merge them in the future.)

Docker

Dependencies

• Onehot, ProtTrans, and MSA Transformer embedded sequences;
• Docker Desktop 4.27.2 or higher;

Installing

• Pull the Docker image from DockerHub

  docker pull dimeng851/punch2:v1

Executing program

• RUN the following command:

  Replace
  CONTAINER_NAME - anyname you like;
  PATH_TO_INPUT_FASTA - path to input file, which is ONE FASTA file including all query sequences;
  PATH_TO_ONEHOT - a folder which includes all ONEHOT embedded sequences;
  PATH_TO_MSATRANS - a folder which includes all MSA Transformer embedded sequences;
  PATH_TO_PROTTRANS - a folder which includes all protTrans embedded sequences;
  PATH_OUTPUT - a folder which will be used to save all outputs, including: a. timings.csv; b. disorder folder, where will keep all the prediction resulds.

  docker run -d \
  -it \
  --name [CONTAINER_NAME] \
  --mount type=bind,source=[PATH_TO_INPUT_FASTA],target=/punch2/data/input.fasta \
  --mount type=bind,source=[PATH_TO_ONEHOT],target=/punch2/data/onehot \
  --mount type=bind,source=[PATH_TO_MSATRANS],target=/punch2/data/msaTrans \
  --mount type=bind,source=[PATH_TO_PROTTRANS],target=/punch2/data/protTrans \
  --mount type=bind,source=[PATH_OUTPUT],target=/punch2/output \
  dimeng851/punch2:v1

  An example:

  docker run -d \
  -it \
  --name punch2_con \
  --mount type=bind,source=/home/dimeng/caid3/test_idr.fasta,target=/punch2/data/input.fasta \
  --mount type=bind,source=/home/dimeng/project/idr/data/caid/features/onehot,target=/punch2/data/onehot \
  --mount type=bind,source=/home/dimeng/project/idr/data/caid/features/msaTrans,target=/punch2/data/msaTrans \
  --mount type=bind,source=/home/dimeng/project/idr/data/caid/features/protTrans,target=/punch2/data/protTrans \
  --mount type=bind,source=/home/dimeng/caid3/punch_idr_output,target=/punch2/output \
  dimeng851/punch2:v1

• Find the results in OUTPUT folder.

Contact & Help 📩

Email Di.

di.meng@ucdconnect.ie

Authors

📬 Di Meng - di.meng@ucdconnect.ie
📬 Gianluca Pollastri - gianluca.pollastri@ucd.ie

Project

https://github.com/deemeng/punch2