ENDscript 2.0

ENDscript 2.0 extracts and visualizes comprehensive protein structural information from primary sequence to quaternary assemblies, integrating sequence alignments, residue conservation, secondary structure, accessibility, hydropathy, intermolecular contacts, and 3D representations.

Key Features:

• Integration with ESPript 3: Leverages ESPript version 3 for sequence alignment rendering, enabling handling of large datasets with reduced computation time.
• Automated analysis and visualization: From a single Protein Data Bank (PDB) entry or file, generates multiple sequence alignments of homologous proteins colored by residue conservation and produces high-quality figures.
• Comprehensive structural annotation: Overlays experimental secondary-structure elements and annotates conserved residues, solvent accessibility, hydropathy, and intermolecular contacts on alignments.
• Interactive 3D visualization: Produces interactive 3D representations via PyMOL and can superimpose similar 3D structures to visualize sequence and structure conservation.
• Adaptive algorithm: Implements an adaptive and rigorous algorithm allowing parameter modification for analysis fine-tuning.
• Platform integration: Integrates biochemical and structural data from external bioinformatics tools to provide coordinated 2D and 3D representations.

Scientific Applications:

• Sequence–structure correlation: Correlates one-dimensional (sequence), two-dimensional (alignment), and three-dimensional (structure) information to interpret functional and evolutionary features.
• Homology and evolutionary analysis: Facilitates identification and analysis of homologous proteins via BLAST- and Clustal-derived alignments and PHYLODENDRON outputs.
• Protein domain and secondary-structure analysis: Supports analysis of protein domains and the prediction/annotation of secondary structures using DSSP-derived annotations.
• Intermolecular interaction analysis: Enables analysis and visualization of intermolecular contacts and residue conservation across superposed structures.

Methodology:

Processes PDB entries/files and integrates BLAST, Clustal, PHYLODENDRON, DSSP, CNS, MOLSCRIPT, PROFIT, ESPript 3 and PyMOL to generate sequence alignments, secondary-structure annotations, structural overlays and coordinated 2D/3D renderings.