PRIMO: An Interactive Homology Modeling Pipeline

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homo...

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Vydané v:PloS one Ročník 11; číslo 11; s. e0166698
Hlavní autori: Hatherley, Rowan, Brown, David K., Glenister, Michael, Tastan Bishop, Özlem
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States Public Library of Science 17.11.2016
Public Library of Science (PLoS)
Predmet:
Algorithms
Automation
Binding sites
Biochemistry
Bioinformatics
Biology and Life Sciences
Comparative analysis
Computer and Information Sciences
Consortia
Coordination compounds
Employment
Fourier transforms
Homology
Internet
Ligands
Mathematical models
Model accuracy
Modelling
Models, Molecular
Monomers
Parameter modification
Physical sciences
Programming Languages
Proteins
Quality
Research and Analysis Methods
Sequence Alignment
Servers
Software
Structural Homology, Protein
Three dimensional models
User-Computer Interface
South Africa
Africa
ISSN:1932-6203, 1932-6203
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Popis
Shrnutí:The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO's automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/.
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Competing Interests: The authors have declared that no competing interests exist.
Conceptualization: ÖTB. Funding acquisition: ÖTB. Methodology: RH DKB. Software: RH DKB MG. Supervision: ÖTB. Validation: RH DKB ÖTB. Writing – original draft: RH DKB ÖTB. Writing – review & editing: RH DKB MG ÖTB.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0166698