Bujnicki Lab Tools

Bujnicki Lab Tools provides integrated sequence alignment, phylogenetic analysis, experimental-data integration, and computational modeling to generate atomic-level 3D structural models of RNA, proteins, and RNA–protein complexes for RNA structure–function studies.

Key Features:

• Sequence alignment (BLAST): Compares nucleotide or protein sequences against sequence databases to identify regions of similarity.
• Iterative sequence search (PSI-BLAST): Performs iterative searches that build a position-specific scoring matrix (PSSM) to detect distant evolutionary relationships.
• PhyloTable: Constructs and analyzes phylogenetic trees from sequence data for evolutionary analysis.
• Hydrodynamic techniques: Uses methods such as analytical ultracentrifugation to assess sample homogeneity.
• Solution scattering measurements: Employs solution X-ray and neutron scattering to obtain low-resolution shape information about macromolecules and complexes.
• Computational modeling: Integrates experimental data with computational algorithms to generate atomic-level 3D structural models of RNA, proteins, and RNA–protein complexes.
• Quality control pipeline: Emphasizes assessment of aggregation-free, monodispersed preparations to ensure reliability of scattering-based structural determinations.

Scientific Applications:

• RNA structural biology: Elucidates RNA structure–function relationships through combined experimental and computational approaches.
• Modeling RNA–protein complexes: Produces atomic-level models of RNA–protein assemblies by integrating scattering and hydrodynamic data with modeling.
• Bridging low- and high-resolution data: Combines solution scattering and hydrodynamic measurements with computational modeling to translate low-resolution shapes into atomic models.
• Phylogenetic analysis: Infers evolutionary relationships and constructs evolutionary trees from sequence alignments.
• Sample quality assessment: Applies hydrodynamic and scattering measurements to verify sample homogeneity for structural experiments.

Methodology:

Computational methods include sequence alignment with BLAST, iterative PSI-BLAST searches building a position-specific scoring matrix, phylogenetic tree construction via PhyloTable, and computational modeling that integrates solution scattering and hydrodynamic data to generate atomic-level 3D structures.