BioInfo3D

BioInfo3D provides comprehensive computational analysis of protein 3D structures, including flexible structural alignment, multiple-structure comparison, and docking-based interaction prediction for studying conformational dynamics and molecular recognition.

Key Features:

• FlexProt: Performs flexible structural alignments while detecting hinge regions and aligning rigid subparts without prior knowledge of hinge locations.
• MultiProt: Performs simultaneous comparison of multiple protein structures to identify common substructures and structural similarities.
• MASS: Performs simultaneous multiple-structure comparison to analyze structural similarities and differences across a set of proteins.
• PatchDock: Predicts interactions between proteins and between proteins and small molecules using docking-based interaction prediction.
• Input formats: Accepts protein PDB codes and uploaded protein structure files as input.

Scientific Applications:

• Protein dynamics analysis: Detection of hinge regions and rigid subparts to study conformational changes and structural flexibility.
• Molecular recognition: Prediction of protein–protein and protein–small molecule interactions to investigate molecular recognition processes.
• Comparative structural analysis: Identification of structural similarities and differences to infer evolutionary relationships and functional analogies.
• Structural biology and molecular modeling: Support for analyses relevant to structural interpretation, modeling, and hypothesis generation in structural biology.

Methodology:

Computational methods explicitly include FlexProt flexible structural alignment with hinge-region detection and rigid-part alignment, MultiProt and MASS simultaneous multiple-structure comparison, and PatchDock docking-based interaction prediction; inputs are protein PDB codes or uploaded protein structures.