ArticleComputational and mathematical methods in medicine2013
Space constrained homology modelling: the paradigm of the RNA-dependent RNA polymerase of dengue (type II) virus.
Article in Computational and mathematical methods in medicine, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 23 citations in OpenAlex.
- Chikungunya nsP4 homology modeling reveals a common motif with Zika and Dengue RNA polymerases as a potential therapeutic target.Journal of molecular modeling · 2021Article
- Ebola Virus Disease and Current Therapeutic Strategies: A Review.Advances in experimental medicine and biology · 2021Review
- Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic.Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association · 2020Review
- Dark Suite: a comprehensive toolbox for computer-aided drug design.EMBnet.journal · 2020Article
- Antibody Clustering Using a Machine Learning Pipeline that Fuses Genetic, Structural, and Physicochemical Properties.Advances in experimental medicine and biology · 2020Article
- Drugena: A Fully Automated Immunoinformatics Platform for the Design of Antibody-Drug Conjugates Against Neurodegenerative Diseases.Advances in experimental medicine and biology · 2020Article
- Article
- Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces.BMC structural biology · 2016Article
- Article
- A series of Notch3 mutations in CADASIL; insights from 3D molecular modelling and evolutionary analyses.Journal of molecular biochemistry · 2014Article
- Structural models for the design of novel antiviral agents against Greek Goat Encephalitis.PeerJ · 2014Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein structure is more conserved than sequence in nature. In this direction we developed a novel methodology that significantly improves conventional homology modelling when sequence identity is low, by taking into consideration 3D structural features of the template, such as size and shape. Herein, our new homology modelling approach was applied to the homology modelling of the RNA-dependent RNA polymerase (RdRp) of dengue (type II) virus. The RdRp of dengue was chosen due to the low sequence similarity shared between the dengue virus polymerase and the available templates, while purposely avoiding to use the actual X-ray structure that is available for the dengue RdRp. The novel approach takes advantage of 3D space corresponding to protein shape and size by creating a 3D scaffold of the template structure. The dengue polymerase model built by the novel approach exhibited all features of RNA-dependent RNA polymerases and was almost identical to the X-ray structure of the dengue RdRp, as opposed to the model built by conventional homology modelling. Therefore, we propose that the space-aided homology modelling approach can be of a more general use to homology modelling of enzymes sharing low sequence similarity with the template structures.
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