T-Analyst

T-Analyst analyzes molecular dynamics (MD) trajectories using internal bond-angle-torsion coordinates to detect and quantify internal torsional movements such as side-chain rotations and characterize protein conformational dynamics.

Key Features:

• Internal Bond-Angle-Torsion Coordinates: Represents conformational changes using internal bond-angle-torsion coordinates instead of Cartesian coordinates to highlight torsional motions.
• Entropy Calculation and Rotameric State Analysis: Computes entropy of dihedral angles and automatically detects and corrects angle periodicity to determine rotameric states.
• Clustering and Hinge Motion Detection: Clusters multiple conformations to identify representative states and detects dihedral rotations that contribute to hinge-like motions.
• Correlation Mapping: Generates correlation maps of selected dihedrals to reveal correlated movements within protein structures.
• Protein Flexibility Analysis: Quantifies changes in protein flexibility across different states to assess allosteric regulation and conformational transitions.
• Molecular Docking Preparation: Selects representative conformations to provide relevant structural states for molecular docking studies.

Scientific Applications:

• Protein Flexibility and Conformational Studies: Characterizes torsional flexibility and conformational transitions in proteins from MD data.
• Enzyme Mechanism Investigation: Analyzes dihedral motions and rotamer distributions relevant to catalytic mechanisms.
• Drug Design and Molecular Docking: Provides representative conformations and torsional analysis to inform ligand binding and docking studies.
• Protein–Protein Interaction Analysis: Evaluates conformational changes and correlated dihedral movements that influence complex formation.

Methodology:

T-Analyst is implemented in Perl and transforms MD trajectory data into internal bond-angle-torsion coordinates; it computes dihedral-angle entropies, detects and corrects angle periodicity for rotamer assignment, performs clustering to select representative conformations, detects dihedral rotations and hinge-like motions, and constructs correlation maps of selected dihedrals.