MultiProt

MultiProt performs fully automated multiple structural alignments of protein structures to identify common geometrical cores and high-scoring partial matches among input molecules.

Key Features:

• Fully automated multiple structural alignment: Performs automated multiple structural alignments of protein structures without relying on pairwise-only solutions.
• Simultaneous superposition: Derives alignments through simultaneous superpositions of input molecules rather than successive pairwise superpositions.
• Partial multiple alignment detection: Detects high-scoring partial multiple alignments for any possible number or subset of molecules within a dataset.
• Sequence order-independence: Produces alignments that do not depend on maintaining sequence order.
• Common geometrical core identification: Identifies common geometrical cores among proteins while allowing some input molecules to be excluded from a given alignment.
• Binding-site and interface alignment: Aligns binding sites and protein-protein interfaces across multiple structures.

Scientific Applications:

• Partial alignment of hinge-bent domains: Identifies common structural elements within hinge-bent domains to study conformational mechanisms.
• Identification of functional groups of G-proteins: Discerns structural characteristics that define different functional groups within G-protein families.
• Analysis of binding sites: Compares binding-site geometries across multiple proteins to inform ligand interaction and drug-target analyses.
• Protein-protein interface alignment: Aligns protein-protein interfaces to study complex formation and interaction networks.

Methodology:

Derives alignments by simultaneous superpositions of input molecules, scores and detects high-scoring partial multiple alignments, identifies common geometrical cores, and generates sequence order-independent alignments that may exclude some molecules from a given alignment.