GOR

An implementation of the GOR (Garnier-Osguthorpe-Robson) protein secondary structure prediction algorithm in Java, supporting methods GOR1 through GOR5. Predicts three secondary structure states, those being coil (C), beta-strand (E), and helix (H), for each amino acid in a given sequence.

Build

Requires Java 21.

./build_all.sh

Produces three JARs in out/artifacts/, for training, prediction and validation respectively.

Usage

Training

java -jar train.jar --db <training_file> --method <gor1|gor3|gor4|gor5> --model <output_model>

Prediction

java -jar predict.jar --model <model_file> --seq <sequence_file> [--probabilities] [--colored]

Validation

java -jar validate.jar --db <validation_file> --method <gor1|gor3|gor4|gor5> --model <model_file>

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License

MIT License