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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances.

Russell B Davidson¹, Jess Woods¹, T Chad Effler¹

¹Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.

Bioinformatics (Oxford, England)

|May 5, 2022

Summary

This summary is machine-generated.

OpenMDlr is a new, open-source Python package for protein structure modeling using inter-atomic distances. This user-friendly tool simplifies modeling from experimental data and refining predicted protein structures efficiently.

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Area of Science:

Computational Biology
Structural Bioinformatics
Biophysics

Background:

Accurate protein structure modeling is crucial for understanding biological function and disease.
Existing methods for modeling protein structures from experimental data or predicted models can be complex and computationally intensive.
There is a need for accessible, general-purpose software to facilitate protein structure modeling.

Purpose of the Study:

To introduce OpenMDlr, an open-source Python package designed for protein structure modeling.
To provide a user-friendly tool for modeling protein structures from pairwise atomic distances and dihedral angles.
To enable efficient utilization of modern biomolecular force fields and multi-core processing.

Main Methods:

Development of an open-source Python package, OpenMDlr.
Implementation of a user-friendly input format for specifying inter-atomic distances and dihedral angles.
Integration with modern biomolecular force fields and optimization for multi-core computation.

Main Results:

OpenMDlr facilitates protein structure modeling from experimental data and refinement of predicted structures.
The package supports modeling based on pairwise atomic distances and optional dihedral angles.
OpenMDlr is designed for ease of installation and efficient computation.

Conclusions:

OpenMDlr offers an accessible and efficient solution for protein structure modeling.
The software supports diverse modeling approaches, including those based on experimental data.
OpenMDlr promotes open-source collaboration in structural bioinformatics.