Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts

Patrik Björkholm, Pawel Daniluk, Andriy Kryshtafovych, Krzysztof Fidelis, Robin Andersson, Torgeir R. Hvidsten

Abstract: Correct prediction of residue–residue contacts in proteins that lack good templates with known structure would take ab initio protein structure prediction a large step forward. The lack of correct contacts, and in particular long-range contacts, is considered the main reason why these methods often fail.