SPECS: Integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural models.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2020
2020
Historique:
received:
22
07
2019
accepted:
11
01
2020
entrez:
14
2
2020
pubmed:
14
2
2020
medline:
24
4
2020
Statut:
epublish
Résumé
Significant advancements in the field of protein structure prediction have necessitated the need for objective and robust evaluation of protein structural models by comparing predicted models against the experimentally determined native structures to quantitate their structural similarities. Existing protein model versus native similarity metrics either consider the distances between alpha carbon (Cα) or side-chain atoms for computing the similarity. However, side-chain orientation of a protein plays a critical role in defining its conformation at the atomic-level. Despite its importance, inclusion of side-chain orientation in structural similarity evaluation has not yet been addressed. Here, we present SPECS, a side-chain-orientation-included protein model-native similarity metric for improved evaluation of protein structural models. SPECS combines side-chain orientation and global distance based measures in an integrated framework using the united-residue model of polypeptide conformation for computing model-native similarity. Experimental results demonstrate that SPECS is a reliable measure for evaluating structural similarity at the global level including and beyond the accuracy of Cα positioning. Moreover, SPECS delivers superior performance in capturing local quality aspect compared to popular global Cα positioning-based metrics ranging from models at near-experimental accuracies to models with correct overall folds-making it a robust measure suitable for both high- and moderate-resolution models. Finally, SPECS is sensitive to minute variations in side-chain χ angles even for models with perfect Cα trace, revealing the power of including side-chain orientation. Collectively, SPECS is a versatile evaluation metric covering a wide spectrum of protein modeling scenarios and simultaneously captures complementary aspects of structural similarities at multiple levels of granularities. SPECS is freely available at http://watson.cse.eng.auburn.edu/SPECS/.
Identifiants
pubmed: 32053611
doi: 10.1371/journal.pone.0228245
pii: PONE-D-19-20679
pmc: PMC7018003
doi:
Substances chimiques
Proteins
0
Carbon
7440-44-0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0228245Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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