SHREC2020 track: Multi-domain protein shape retrieval challenge

Florent Langenfeld*, Yuxu Peng, Yu Kun Lai, Paul L. Rosin, Tunde Aderinwale, Genki Terashi, Charles Christoffer, Daisuke Kihara, Halim Benhabiles, Karim Hammoudi, Adnane Cabani, Feryal Windal, Mahmoud Melkemi, Andrea Giachetti, Stelios Mylonas, Apostolos Axenopoulos, Petros Daras, Ekpo Otu, Reyer Zwiggelaar, David HunterYonghuai Liu, Matthieu Montès

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Citations (SciVal)
191 Downloads (Pure)


Proteins are natural modular objects usually composed of several domains, each domain bearing a specific function that is mediated through its surface, which is accessible to vicinal molecules. This draws attention to an understudied characteristic of protein structures: surface, that is mostly unexploited by protein structure comparison methods. In the present work, we evaluated the performance of six shape comparison methods, among which three are based on machine learning, to distinguish between 588 multi-domain proteins and to recreate the evolutionary relationships at the proteinand species levels of the SCOPe database. The six groups that participated in the challenge submitted a total of 15 sets of results. We observed that the performance of all the methods significantly decreases at the species level, suggesting that shape-only protein comparison is challenging for closely related proteins. Even if the dataset is limited in size (only 588 proteins are considered whereas more than 160,000 protein structures are experimentally solved), we think that this work provides useful insights into the current shape comparison methods performance, and highlights possible limitations to large-scale applications due to the computational cost.

Original languageEnglish
Pages (from-to)189-198
Number of pages10
JournalComputers and Graphics (Pergamon)
Early online date01 Aug 2020
Publication statusPublished - 01 Oct 2020


  • 3D shape analysis
  • 3D shape descriptor
  • 3D shape matching
  • 3D shape retrieval
  • Protein shape


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