MulPBA

MulPBA performs multiple structural alignments of protein structures using a structural alphabet derived from backbone dihedral angles to enable comparative analysis of protein function, evolution, and architecture.

Key Features:

• Structural alphabet representation: Describes backbone conformation via dihedral angles to produce a sequence-like representation that enables application of sequence alignment methods.
• Iterative refinement of superposition: Employs an iterative refinement process to improve structural superposition, surpassing rigid-body alignment and being comparable to flexible structure comparison approaches.
• Sequence alignments and 3D superposition: Produces multiple sequence alignments and superposed 3D structures for the input protein chains.
• Quality measures and relatedness indicators: Computes multiple global quality measures and a distance dendrogram to indicate relatedness among compared protein structures.
• Output formats: Provides superimposed structures in PDB format for downstream analysis.

Scientific Applications:

• Protein function and architecture analysis: Comparative alignments aid identification of conserved structural features relevant to protein function and architecture.
• Evolutionary relationship inference: Distance dendrograms and alignments support analyses of structural relatedness and evolutionary pathways.
• Conserved region and motif identification: Alignments enable detection of conserved regions and functional motifs across multiple structures.
• Structure-guided targeting and mutagenesis: Superposed structures and quality metrics inform structural sites of interest for drug targeting or mutagenesis studies.

Methodology:

Represent backbone conformation with a structural alphabet based on dihedral angles, convert structures to a sequence-like form, apply sequence alignment methods, perform iterative refinement to enhance superposition, compute global quality measures and a distance dendrogram, and generate sequence alignments and superposed structures in PDB format.