Gene

Computational science

Workflow

Biology

Principal component analysis

R package

Set (abstract data type)

Biochemistry

Sequence analysis

Data mining

Computer science

Protein superfamily

Protein structure

Computational biology

Genetics

Bioinformatics

Database

Sequence (biology)

Sequence database

Artificial intelligence

Protein structure prediction

Sequence alignment

Protein structure database

Programming language

Peptide sequence

Protein Science

Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D-eddm package supports both experimental and theoretical simulation-generated structures, is integrated with other methods for dissecting sequence-structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/.

The <scp>Bio3D</scp> packages for structural bioinformatics

The Bio3D packages for structural bioinformatics