Dataset Information

3DFI: a pipeline to infer protein function using structural homology.

ABSTRACT:

Motivation

Inferring protein function is an integral part of genome annotation and analysis. This process is usually performed in silico, and most in silico inferences are based on sequence homology approaches, which can fail when in presence of divergent sequences. However, because protein structures and their biological roles are intertwined, protein function can also be inferred by searching for structural homology. Many excellent tools have been released in recent years with regards to protein structure prediction, structural homology searches and protein visualization. Unfortunately, these tools are disconnected from each other and often use a web server-based approach that is ill-suited to high-throughput genome-wide analyses. To help assist genome annotation, we built a structural homology-based pipeline called 3DFI (for tridimensional functional inference) leveraging some of the best structural homology tools. This pipeline was built with simplicity of use in mind and enables genome-wide structural homology inferences.

Availability and implementation

3DFI is available on GitHub https://github.com/PombertLab/3DFI under the permissive MIT license. The pipeline is written in Perl and Python.

SUBMITTER: Julian AT

PROVIDER: S-EPMC9162058 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

3DFI: a pipeline to infer protein function using structural homology.

Julian Alexander Thomas AT Dos Santos Anne Caroline Mascarenhas ACM Pombert Jean-François JF

Bioinformatics advances 20211110 1

<h4>Motivation</h4>Inferring protein function is an integral part of genome annotation and analysis. This process is usually performed <i>in silico</i>, and most <i>in silico</i> inferences are based on sequence homology approaches, which can fail when in presence of divergent sequences. However, because protein structures and their biological roles are intertwined, protein function can also be inferred by searching for structural homology. Many excellent tools have been released in recent years ...[more]

PMID: 35664289

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Project description: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/.

Dataset Information

3DFI: a pipeline to infer protein function using structural homology.

Motivation

Availability and implementation

Publications

3DFI: a pipeline to infer protein function using structural homology.

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