Bios2cor: an R package integrating dynamic and evolutionary correlations to identify functionally important residues...

Area of Science:

• Computational Biology
• Bioinformatics
• Structural Biology

Background:

• Identifying functionally important residues is crucial for understanding protein mechanisms.
• Both dynamic correlations in protein sidechain motions (from molecular dynamics simulations) and evolutionary correlations (from multiple sequence alignments) can highlight these key residues.

Purpose of the Study:

• To develop a novel R package, Bios2cor, for investigating and integrating analyses of dynamic and evolutionary correlations in proteins.
• To provide a unified framework for uncovering functionally important residues.

Main Methods:

• The Bios2cor R package was developed.
• It accepts multiple sequence alignments (MSAs) or molecular dynamics (MD) trajectories as input.
• The package computes correlation/covariation scores between positions in MSAs or between sidechain dihedral angles/rotamers in MD trajectories.

Main Results:

• Bios2cor offers a unique framework for analyzing protein residue importance.
• The package facilitates the computation of correlation and covariation scores from both MD simulations and MSAs.
• It includes tools for data analysis, visualization, and interpretation.

Conclusions:

• Bios2cor provides a comprehensive approach to identify functionally important protein residues by combining dynamic and evolutionary information.
• The package enhances the investigation of protein function through integrated computational analyses.
• Bios2cor is available as an R package from CRAN.