Recently two main types of methods are being used for protein loop predictions- knowledge based and ab-initio. Till now, knowledge based methods utilize protein sequences of similiar lengths for prediction of protein loops. Ab-initio methods computationally generate protein structures.
Marks et. al. (2017) have made a software called sphinx which utilizes both these methods to generate structures. It can be used for difficult tasks like antibody predictions.The software is available at the following URL:http://opig.stats.ox.ac.uk/webapps/sphinx.
Marks C et.al.(2017) Sphinx: Merging knowlwdge - based and ab initio approaches to improve protein loop prediction. Bioinformatics 33 (9):1346-1353