CHOMP: Getting Started

From SHARPEN

Note: Most of the example scripts listed here were put together with an early version of SHARPEN. Updating to the latest syntax is underway. We are accumulating a comparable list of scripts with the latest syntax here:

New Tutorials

Contents 1 Basic 2 Intermediate 3 Advanced 4 Projects

Basic

1. Linux Pocket Guide
2. Basic python scripting
3. Python and Matlab
4. Parse and score a pdb
5. Optimize all rotamers with entirely default settings
6. Walkthrough functions with iPython
7. Repack specific residues
8. Repack with multiple packers

Intermediate

1. Score protein as is, after rotamerization
2. Energy decomposition
3. Score pdb and detect steric clashes
4. Repack a set of proteins
5. Report ramachandran outliers
6. Alter simulated annealing algorithm
7. Alanine scanning
8. Optimize protein complex
9. Binding interaction energy
10. Monte Carlo search
11. Simulated annealing via Monte Carlo
12. Brute force search
13. Monte Carlo with multiple energy graphs
14. Visualize rotamers
15. CHOMP tutorial: backbone geometry
16. Visualize centroids
17. Customize the rotamer generator
18. Understanding the rotamer generator
19. Backbone rebuild post residue deletion
20. Backbone rebuild post residue insertion
21. Build a peptide from scratch

Advanced

1. Repack with 90% VDW radii
2. Repack part of a larger system
3. Load two complexed proteins and optimize all rotamers
4. Adaptive rotamer discretization
5. Calculate atom pairwise repulsion between residues
6. Divide and conquer rotamer optimization
7. Rebuild part of the backbone
8. Manual hypergraph construction and simulated annealing
9. Convert an energy graph into a hypergraph
10. Save a hypergraph to disk
11. Calculating a ranked list of solutions
12. Track number crunching
13. Convert a python script to C++
14. backbone tweak Monte Carlo
15. CHOMP tutorial: SPR
16. Visualize an energy graph
17. Protein design
18. Identify residues that might hydrogen bond to a target residue
19. Storing large datasets with pytables
20. Dead-end elimination of Goldstein singles
21. Python implementation of belief propagation
22. Python implementation of the all-atom Rosetta terms

Projects

1. CHOMP project: identify recombination sites that minimize the number of inter-block contacts
2. CHOMP project: polarizable protein repacking
3. CHOMP project: redesign dimer orthogonal pair