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molecular file formats in bioinformatics

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molecular file formats in bioinformatics

  1. 1. MOLECULAR FILE FORMATS The two mostly used molecular file formats are as follows: PDB File format CHARMm file format 2
  2. 2. SECTIONS AND RECORDS IN PDB FILE FORMAT Title section Remarks section Primary structure section Heterogenic section Secondary structure section Connectivity/annotation section Miscellaneous feature section Crystallographic and coordinate transformation section coordinate transformation section Coordinate section Connectivity section Bookkeeping section 3
  3. 3. CHARMM FILE FORMAT Molecular mechanisms and molecular dynamics software Empirical potential energy function Energy minimization Molecular dynamics simulation Vibrational analysis Thermodynamic analysis Quantum mechanics and molecular mechanics calculation Title line begins with a * and also in the next line ends with a *
  4. 4. MOLECULAR CONVERSION TOOLS Pdb2cif Cif2pdb Babel Into Cham Mol2Mol 5
  5. 5. BABEL Interconverts number of molecular file formats Used in molecular modeling Assigning hybridization Bond order Connectivity in the input file when its not already present
  6. 6. MOL2MOL File formats inter-conversion Reads about 50 file formats and sub formats
  7. 7. THANKS FOR YOUR PATEINCE

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