molecular file formats in bioinformatics
TRANSCRIPT
MOLECULA
R FILE
FORMAT
S
MOLECULAR FILE FORMATS
The two mostly used molecular file formats are as follows:
PDB File format
CHARMm file format
2
SECTIONS AND RECORDS IN PDB FILE FORMATTitle 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
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 *
MOLECULAR CONVERSION TOOLS
Pdb2cif
Cif2pdb
Babel
Into Cham
Mol2Mol
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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
MOL2MOL
File formats inter-conversion
Reads about 50 file formats and sub formats
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