PepBuild

PepBuild constructs capped and uncapped peptide and protein sequences with defined secondary and tertiary structures to generate PDB-format models for structural design and molecular simulation.

Key Features:

• Structure-Based Design: Constructs peptides or proteins by selecting amino acid residues that conform to specified secondary-structure elements.
• Customizable Torsional Angles: Accepts user-specified torsional angles to define backbone conformation.
• Protecting Group Addition: Adds protecting groups at the N-terminal and/or C-terminal ends of peptides.
• Side Chain Optimization: Optimizes amino-acid side-chain conformations using rotameric libraries.
• Sequence Capping Options: Supports design of both capped and uncapped peptide and protein sequences.
• PDB Output: Renders resulting structures in PDB (Protein Data Bank) format for downstream use.

Scientific Applications:

• Peptide and Protein Synthesis Design: Provides structural models to assist planning and design of peptide and protein synthesis.
• Molecular Simulation Input: Produces PDB-format models suitable as inputs for molecular simulation programs and computational analyses.
• Protein Engineering and Structural Biology: Enables construction of models for protein engineering and structural biology investigations.

Methodology:

Accepts specified structural parameters such as selected residues and torsional angles, optimizes side-chain conformations using rotameric libraries, incorporates specified protecting groups, and outputs the resulting structure in PDB format.