FragBuilder

FragBuilder generates peptide model structures and prepares them for quantum mechanical (QM) calculations by enabling conformational specification, conformer sampling, MMFF94 geometry optimization, and export of QM program input.

Key Features:

• Conformation specification: Manual specification of particular peptide conformations for targeted modeling.
• Conformational sampling: Sampling of backbone and side-chain rotamer conformations from continuous distributions.
• Geometry optimization: Geometry optimization using the MMFF94 molecular mechanics force field.
• File export and QM input generation: Export of optimized structures to XYZ and PDB formats and direct generation of input files for quantum chemistry programs.
• Open Babel compatibility: Integration with Open Babel with a noted potential for dihedral angle issues in certain Open Babel releases.

Scientific Applications:

• QM calculation setup: Preparation of peptide structures and input files for quantum mechanical calculations.
• Electronic structure analysis: Support for studies of electronic structure, including reaction mechanism investigations.
• Binding and affinity studies: Facilitation of calculations relevant to binding affinity predictions.
• Conformational studies: Exploration of peptide backbone and side-chain conformational space to study structural flexibility relevant to peptide chemistry, drug design, and molecular dynamics.

Methodology:

Manual specification or automated sampling of backbone and side-chain rotamer conformations from continuous distributions, followed by geometry optimization with the MMFF94 force field and export as XYZ/PDB or quantum chemistry program input, with operations that can employ Open Babel (with potential dihedral angle issues in some releases).