BioStructMap

BioStructMap extends sliding-window analyses into three-dimensional protein space to integrate sequence-based features with protein structures for spatially resolved analysis of structural regions and linked genomic sequences.

Key Features:

• 3D Sliding Window Analysis: Applies sliding-window analysis in three dimensions by partitioning protein structures into overlapping spatial regions to examine spatially distributed data.
• Custom Function Integration: Allows application of user-defined functions to spatially aggregated data within those 3D regions for tailored analyses.
• Genomic Sequence Mapping: Maps underlying genomic sequences onto protein structures to link codons with spatial segments and enable genetic-based analyses of selection pressures.

Scientific Applications:

• Protein Structure Analysis: Identifies structural motifs and regions relevant to function or stability using spatially resolved analyses.
• Evolutionary Biology: Enables investigation of how genetic variation and selection pressures manifest in protein structural contexts by linking genomic sequences to structure.
• Structural Genomics: Facilitates integration of sequence and structural information for comprehensive analysis of protein structure datasets.

Methodology:

Implemented in Python; extends one-dimensional sliding-window analysis into three dimensions by partitioning protein structures into overlapping spatial regions and applying user-defined functions to those segments, and maps genomic sequences to structural positions to associate codons with spatial regions.