From Jacobson Lab Wiki
PLOP (Protein Local Optimization Program) is a program for protein modeling using all-atom energy functions. It includes a number of algorithms developed by Matt Jacobson and collaborators, including multiscale Truncated Newton minimization, side chain optimization, loop prediction, and the prediction of helix positions and orientations. It has been successfully used to refine homology models, relax protein-ligand complexes (i.e., induced fit effects), build models from experimental data, and investigate functionally relevant loop motions, due to post-translational modification and ligand binding.
PLOP was originally written by Matthew P. Jacobson, in collaboration with Richard A. Friesner, at Columbia University beginning in September 2000. Since September 2002, the code has been maintained at UCSF, with contributions from both UCSF and Columbia. The program has been licensed by both universities to Schrödinger, Inc. for commercial distribution as part of the PRIME (PRotein Integrated Modeling Environment) package.
Recently, Prof. Victor Guallar and his group at Washington University, St. Louis, implemented their PELE method in the PLOP package. Combining protein structure prediction algorithms and Metropolis Monte Carlo techniques, PELE provides a novel method to explore the long time dynamics energy landscapes of protein sized systems represented by all-atom force fields. The core of the technique is based on a steered localized perturbation followed by side chain sampling as well as minimization cycles. Further details are available here.
 Getting Started
 Specific Tasks
- Loading PDB files
- Writing PDB files
- Plop Commands
- Predicting/changing protonation states
- Side chain optimization
- Loop prediction
- Helix prediction
- Homology model construction
- Plop Molecular Dynamics
- Plop Monte Carlo
- 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):