How can I compute energy from a protein PDB file?

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SUMMARY

To compute energy from a protein PDB file, users can utilize the coordinates within the file, although the absence of the `CONECT` field in some PDB files, such as 4OSK.pdb, may complicate the process. The discussion emphasizes the need for alternative methods to extract connectivity information when the `CONECT` field is missing. Participants suggest leveraging computational tools that can interpret PDB file structures effectively to calculate energy based on atomic coordinates.

PREREQUISITES
  • Understanding of protein structure and PDB file format
  • Familiarity with energy computation formulas in molecular modeling
  • Experience with computational tools for protein analysis
  • Knowledge of software that can handle PDB files, such as PyMOL or Chimera
NEXT STEPS
  • Research how to extract atomic coordinates from PDB files using Python libraries like Biopython
  • Learn about energy computation methods in molecular dynamics simulations
  • Explore the use of PyMOL for visualizing protein structures and calculating interactions
  • Investigate alternative formats or tools that provide connectivity information for PDB files lacking the `CONECT` field
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Researchers in computational biology, biochemists, and molecular modelers who are involved in energy calculations from protein structures.

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TL;DR
Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in the file.

**How can I do that?**
Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in that file.

1696244256611.png


How can I do that?

Sometimes people suggest using the `CONECT` field for that purpose. However, some PDB files do not have this field.

Example: 4OSK.pdb (Crystal structure of TAL effector reveals the recognition between asparagine and guanine)
 

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