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A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

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Published on: October 2, 2012

PRIMO: An Interactive Homology Modeling Pipeline.

Rowan Hatherley¹, David K Brown¹, Michael Glenister¹

¹Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.

|November 18, 2016

Summary

The PRotein Interactive MOdeling (PRIMO) pipeline simplifies protein structure prediction through homology modeling. It offers user engagement and reliable automated results, even without manual intervention.

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Area of Science:

Structural Biology
Computational Biology
Bioinformatics

Background:

Automated protein structure prediction servers simplify calculations but limit user interaction.
Homology modeling is a key technique for predicting protein structures.

Purpose of the Study:

To present the PRotein Interactive MOdeling (PRIMO) pipeline for user-friendly homology modeling of protein monomers.
To allow user engagement in the modeling process while reducing workload.
To enable modeling of protein-ligand and protein-ion complexes.

Main Methods:

Development of the PRIMO pipeline with a user-friendly interface.
Inclusion of default parameters with options for user modification and external input.
Assessment of fully automated capabilities, including alignment programs and refinement levels.
Continuous evaluation of automated scripts by the CAMEO project.

Main Results:

PRIMO eases the multi-step homology modeling process, allowing user engagement at every step.
The pipeline is designed for users of all experience levels, offering suggestions for novices.
PRIMO demonstrates reliability in producing numerous protein models.
Good quality models can be generated automatically when suitable templates are available.

Conclusions:

PRIMO provides a reliable and user-engaging platform for protein homology modeling.
The pipeline offers a base level of accuracy that users can further improve.
PRIMO supports the modeling of complex biological targets including ligands and ions.