Approximate inference and protein-folding

Chen Yanover, Yair Weiss

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

30 Scopus citations


Side-chain prediction is an important subtask in the protein-folding problem. We show that finding a minimal energy side-chain configuration is equivalent to performing inference in an undirected graphical model. The graphical model is relatively sparse yet has many cycles. We used this equivalence to assess the performance of approximate inference algorithms in a real-world setting. Specifically we compared belief propagation (BP), generalized BP (GBP) and naive mean field (MF). In cases where exact inference was possible, max-product BP always found the global minimum of the energy (except in few cases where it failed to converge), while other approximation algorithms of similar complexity did not. In the full protein data set, max-product BP always found a lower energy configuration than the other algorithms, including a widely used protein-folding software (SCWRL).

Original languageAmerican English
Title of host publicationAdvances in Neural Information Processing Systems 15 - Proceedings of the 2002 Conference, NIPS 2002
PublisherNeural information processing systems foundation
ISBN (Print)0262025507, 9780262025508
StatePublished - 2003
Event16th Annual Neural Information Processing Systems Conference, NIPS 2002 - Vancouver, BC, Canada
Duration: 9 Dec 200214 Dec 2002

Publication series

NameAdvances in Neural Information Processing Systems
ISSN (Print)1049-5258


Conference16th Annual Neural Information Processing Systems Conference, NIPS 2002
CityVancouver, BC


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