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Protein Structure Preparation
Lead Finder allows intelligent preparation of protein structure models for docking by enabling:
  • addition of hydrogen atoms to protein's heavy atoms (usually present in PDB files and homology models) according to optimal ionization states of protein residues at a given pH;
  • optimization of polar hydrogen positions with respect to the ligand, substrate and cofactor present in the structure;
  • optimization of side chain orientations of His, Asn and Gln residues for which X-ray analysis can return flipped orientations due to apparent symmetry.
Lead Finder uses an original theoretical approach to assign optimal ionization states of protein residues at arbitrary pH conditions, which is based on the Screened Coulomb Potential (SCP) model12. SCP theory treats microenvironment-dependent energy of electrostatic interactions as a function of local hydrophilicity and degree of solvent exposure. Details of the SCP model implementation in Lead Finder can be found in the Scoring functions section.
Preparation of cytochrome CYP450  3A4 from crude pdb file (pdb id 1w0f): missing (not resolved) residues were automatically build; orientation of Asn, Gln His side chains was optimized; ionization states of residues were fitted for given pH(7.0); positions of flexible hydrogen atoms were energy — optimized.
You can download examples of protein structure preparation using Lead Finder. Each example (archive file) contains description of the task and necessary structure files.
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