FlexProt

FlexProt aligns flexible protein structures by detecting hinge regions and aligning rigid subparts to enable comparative analysis of conformational changes.

Key Features:

• Automatic Detection: Identifies potential flexible hinge regions autonomously during the alignment process.
• Rigid Subpart Alignment: Aligns rigid subparts of protein structures while accommodating flexibility in other regions.
• Robust to Variations: Tolerates insertions or deletions within protein sequences, maintaining alignment accuracy across diverse datasets.

Scientific Applications:

• Benchmarking and datasets: Tested using the database of motions and additional proteins from the same SCOP family, including exhaustive all-against-all flexible structural comparisons of 1329 representatives from various SCOP families.
• C-terminal merozoite surface protein — tissue factor alignment: Produced high-scoring flexible structural alignments between C-terminal merozoite surface protein and tissue factor.
• Class II aminoacyl-tRNA synthase / histocompatibility antigen — neonatal FC receptor alignments: Generated alignments involving class II aminoacyl-tRNA synthase and histocompatibility antigen with neonatal FC receptor.
• C-SRC — HCK comparisons: Performed structural comparisons between tyrosine-protein kinase C-SRC and haematopoetic cell kinase (HCK).
• C-SRC — titine autoinhibited serine kinase domain alignment: Aligned tyrosine-protein kinase C-SRC with the titine protein's autoinhibited serine kinase domain.
• Tissue factor — hormone-binding protein alignment: Aligned tissue factor with hormone-binding protein.
• Research areas: Applicable to studies of protein dynamics and conformational flexibility relevant to drug design, molecular biology, and evolutionary analysis.

Methodology:

FlexProt employs 3-D pattern-matching algorithms combined with graph theoretic techniques for structural comparison, with reported comparisons of ~300-amino-acid proteins taking about 7 seconds on a 400-MHz desktop PC.