ArticleBMC bioinformatics2012
GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed.
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- Exploring the effects of N234 and N343 linked glycans to SARS CoV 2 spike protein pocket accessibility using Gaussian accelerated molecular dynamics simulations.Scientific reports · 2025Article
- Insights into structural vaccinology harnessed for universal coronavirus vaccine development.Clinical and experimental vaccine research · 2024Review
- Improved Thermal Stability of a Novel Acidophilic Phytase.Journal of microbiology and biotechnology · 2024Article
- Investigation of the Mutations in the SARS-CoV-2 Envelope Protein and Its Interaction with the PALS1 by Molecular Docking.Reports of biochemistry & molecular biology · 2024Article
- Multi-epitope Based Peptide Vaccine Candidate AgainstBioinformatics and biology insights · 2024Article
- Complementary Pocket and Network-Based Approach to Search for Spike Protein Allosteric Pocket Sites.ACS omega · 2023Article
- Mce1R of Mycobacterium tuberculosis prefers long-chain fatty acids as specific ligands: a computational study.Molecular diversity · 2023Article
- Multi-epitope vaccine candidates based on mycobacterial membrane protein large (MmpL) proteins againstOpen biology · 2023Article
- Article
- Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.Frontiers in molecular biosciences · 2023Article
- Molecular and functional characterization of protease from psychrotrophic Bacillus sp. HM49 in North-western Himalaya.PloS one · 2023Article
- In silico analysis of a Skp1 protein homolog from the human pathogenJournal of parasitic diseases : official organ of the Indian Society for Parasitology · 2022Article
- Immune epitopes identification and designing of a multi-epitope vaccine against bovine leukemia virus: a molecular dynamics and immune simulation approaches.Cancer immunology, immunotherapy : CII · 2022Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundProtein structures can be reliably predicted by template-based modeling (TBM) when experimental structures of homologous proteins are available. However, it is challenging to obtain structures more accurate than the single best templates by either combining information from multiple templates or by modeling regions that vary among templates or are not covered by any templates.
resultsWe introduce GalaxyTBM, a new TBM method in which the more reliable core region is modeled first from multiple templates and less reliable, variable local regions, such as loops or termini, are then detected and re-modeled by an ab initio method. This TBM method is based on "Seok-server," which was tested in CASP9 and assessed to be amongst the top TBM servers. The accuracy of the initial core modeling is enhanced by focusing on more conserved regions in the multiple-template selection and multiple sequence alignment stages. Additional improvement is achieved by ab initio modeling of up to 3 unreliable local regions in the fixed framework of the core structure. Overall, GalaxyTBM reproduced the performance of Seok-server, with GalaxyTBM and Seok-server resulting in average GDT-TS of 68.1 and 68.4, respectively, when tested on 68 single-domain CASP9 TBM targets. For application to multi-domain proteins, GalaxyTBM must be combined with domain-splitting methods.
conclusionApplication of GalaxyTBM to CASP9 targets demonstrates that accurate protein structure prediction is possible by use of a multiple-template-based approach, and ab initio modeling of variable regions can further enhance the model quality.
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