ArticleJournal of computer-aided molecular design2013
Combining fragment homology modeling with molecular dynamics aims at prediction of Ca²⁺ binding sites in CaBPs.
Article in Journal of computer-aided molecular design, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed, 6 citations in OpenAlex.
- Identification of the Active Principle Conferring Anti-Inflammatory and Antinociceptive Properties in Bamboo Plant.Molecules (Basel, Switzerland) · 2021Article
- Recent progress in structural studies on TMEM16A channel.Computational and structural biotechnology journal · 2020Review
- Two Ca(2+)-Binding Sites Cooperatively Couple Together in TMEM16A Channel.The Journal of membrane biology · 2016Article
- Molecular simulation assisted identification of Ca(2+) binding residues in TMEM16A.Journal of computer-aided molecular design · 2015Article
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Authors and funding
8 authors at 2 institutions in 1 country.
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Abstract
The family of calcium-binding proteins (CaBPs) consists of dozens of members and contributes to all aspects of the cell's function, from homeostasis to learning and memory. However, the Ca²⁺-binding mechanism is still unclear for most of CaBPs. To identify the Ca²⁺-binding sites of CaBPs, this study presented a computational approach which combined the fragment homology modeling with molecular dynamics simulation. For validation, we performed a two-step strategy as follows: first, the approach is used to identify the Ca²⁺-binding sites of CaBPs, which have the EF-hand Ca²⁺-binding site and the detailed binding mechanism. To accomplish this, eighteen crystal structures of CaBPs with 49 Ca²⁺-binding sites are selected to be analyzed including calmodulin. The computational method identified 43 from 49 Ca²⁺-binding sites. Second, we performed the approach to large-conductance Ca²⁺-activated K⁺ (BK) channels which don't have clear Ca²⁺-binding mechanism. The simulated results are consistent with the experimental data. The computational approach may shed some light on the identification of Ca²⁺-binding sites in CaBPs.
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