IntFOLD

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IntFOLD (Integrated Fold Recognition) is fully automated, integrated pipeline for prediction of 3D structure and function from amino acid sequences.^[1] The pipeline is wrapped up and deployed as a publicly-available Web Server.^[2] The core of the server method is quality assessment using built-in accuracy self-estimates (ASE) which improves performance prediction of 3D model using ModFOLD.^[3]

IntFOLD server provides the tertiary structure prediction at a competitive accuracy and combines the cutting edge methods including IntFOLD-TS for generation of 3D models,^[1] ModFOLD for 3D model quality estimation,^[3] ReFOLD for refinement of 3D models,^[4] DisoCLUST for disorder prediction,^[5] DomFOLD for structural domain prediction,^[6] and FunFOLD for protein ligand binding site prediction.^[7] The integration of the tools enables users to reach all related information in a pipeline. IntFOLD Web Server has completed over 200,000 structure predictions since January 2010.^[1]

The only required input is a protein sequence for the prediction of the protein 3D structure and function.^[1] The IntFOLD output is presented via a user-friendly interface for the use of life scientists. The raw data is also formatted in Critical Assessment of Methods for Protein Structure Prediction (CASP) standards with a detailed help page.^[1]

The IntFOLD method was firstly benchmarked in Critical Assessment of Techniques for Protein Structure Prediction 9 (CASP9) and ranked among the top 5.^[8] The IntFOLD server has consolidated its performance in the following CASP experiments ^[1]

Its performance is being continually evaluated in Continuous Automated Model Evaluation (CAMEO) experiment.^[9]

IntFOLD was used to generate 3D models of the SARS-CoV-2 targets for the CASP Commons COVID-19 initiative^[10] and elsewhere ^[11] accelerating the race of vaccines and other therapeutics development with regard to COVID-19 pandemic. In other aspect of chronic diseases, IntFOLD was used to model HEV PCP, an essential protein of Hepatitis E virus causing Hepatitis E disease.^[12] Additionally, IntFOLD was used to model disordered region of the Bovine milk αS2-casein proteins which were implicated in the formation amyloidogenic fibrils some of which are known to be major causes of neurodegenerative diseases.^[13]

IntFOLD has been used in different aspects of food security. For instance, it has been used to model effector proteins molecules that causes fungus in Barley.^[14] Furthermore, it has been applied in modelling several proteins involved in the functioning of key systems in Atlantic salmon, and HaACBP1 protein, which is vital for development and growth of sunflower, a key crop plant used for production of widely used cooking oil.^[15][16] IntFOLD was used to model Chitin proteins in Podosphaera xanthii, a causal agent of fungal disease called cucurbit powdery mildew, which hamper crop productivity.^[17]

IntFOLD has been used as one of the standard server-based methods in validating the performance of some of the newer methods used in prediction of the 3D-protein models. This is important in advancing the structural bioinformatics field.^[18]