ArticlePloS one2014
Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
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- Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Paraquat is an agonist of STIM1 and increases intracellular calcium levels.Communications biology · 2022Article
- S1P defects cause a new entity of cataract, alopecia, oral mucosal disorder, and psoriasis-like syndrome.EMBO molecular medicine · 2022Article
- Tmem178 negatively regulates store-operated calcium entry in myeloid cells via association with STIM1.Journal of autoimmunity · 2019Article
- Review
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- Gammaherpesvirus Tegument Protein ORF33 Is Associated With Intranuclear Capsids at an Early Stage of the Tegumentation Process.Journal of virology · 2015Article
- Differential network analysis reveals dysfunctional regulatory networks in gastric carcinogenesis.American journal of cancer research · 2015Article
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Authors and funding
7 authors.
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Abstract
Many template-based modeling (TBM) methods have been developed over the recent years that allow for protein structure prediction and for the study of structure-function relationships for proteins. One major problem all TBM algorithms face, however, is their unsatisfactory performance when proteins under consideration are low-homology. To improve the performance of TBM methods for such targets, a novel model evaluation method was developed here, and named MEFTop. Our novel method focuses on evaluating the topology by using two novel groups of features. These novel features included secondary structure element (SSE) contact information and 3-dimensional topology information. By combining MEFTop algorithm with FR-t5, a threading program developed by our group, we found that this modified TBM program, which was named FR-t5-M, exhibited significant improvements in predictive abilities for low-homology protein targets. We further showed that the MEFTop could be a generalized method to improve threading programs for low-homology protein targets. The softwares (FR-t5-M and MEFTop) are available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/FRt5M/FRt5M.html.
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