Protein Local Optimization Program: Manual

This "manual" is a work in progress and will continue to evolve as I have bits of time to work on it.

The Basics

PLOP is primarily meant to model proteins, but the current version can also include:

1. monoatomic ions
2. explicit water molecules (e.g., buried or crystallographic waters)
3. general HETATMs (ligands)

With respect to ligands, the current distribution contains about 3000 ligands found in the PDB. Several modified amino acids are also currently supported, including phosphorylated residues. For a complete list of residues supported in the current version, click here.

PLOP currently runs only on Unix and Linux, and jobs are controlled using simple scripts. The path for the script is the only input read from standard input by the program, so you can run it like this:

echo input.dat | plop

where input.dat contains the script (the file could of course be named anything you like). All statements in the script, whether they set parameters or execute a command, are read and performed in strict order. Comment lines can be included; they are started with the character #. Commands can be broken across lines using the continuation character "&" at the end of each line that should continue to the next.

How to Write PLOP Scripts

The basics (read this first)

Loading PDB files

Writing PDB files

Predicting/changing protonation states

Key optimization algorithms:

Minimization

Side chain optimization

Loop prediction

Helix prediction

Homology model construction

Useful analysis tools:

Calculating RMSDs

Hydrogen bond analysis (to be written)

Dihedral angle analysis (to be written)

Secondary structure analysis (to be written)

Identifying problems in structures (to be written)

Energetic analysis (to be written)

Examples

All of the examples use the PDB file 2igd, which you can download here.

Loop Prediction: Input Output

Helix Prediction: Input Output

Homology Model: Input Output