The scripts and input files that accompany this demo can be found in the demos/protocol_captures directory of the Rosetta weekly releases.

This is a protocol capture, and represents the protocol at a fixed point in time. It may not work with the current version of Rosetta.

KEYWORDS: SURFACES GENERAL

Authors

written by Michael Pacella (Graylab), mpacella88@gmail.com

General Description

This demo will describe how to run the C++ version of the RosettaSurface algorithm. The test case shown here will analyze the adsorption of the model peptide LK-alpha to the 104 surface of calcite

Algorithm

Simultaneous optimization of protein rigid-body orientation, backbone and side chain conformations on a solid surface.

Commands

surface_docking<.exe> -database <path/to/database> @input/flags

Input Files

  • lk_alpha_calcite.pdb = input pdb with LK alpha positioned above calcite 104
  • calcite.surf = file containing surface vectors specific to the calcite surface in the input pdb
  • lk_alpha_3mers = 3mer and 9mer fragment files for LK alpha
  • flags = arguments for rosetta surface

Pre-processing

  1. Ensure that the input pdb is properly formatted with the protein appearing before the surface in the input file and belonging to a separate chain

  2. Ensure that the specified surface vectors match the input surface

  3. Ensure that parameter files corresponding to the molecules comprising the surface exist in the rosetta database

Post-processing

(in the directory with output decoys)

  1. GetTop.sh Ads 4
  2. cd TOP4.Ads
  3. PostProcessRS.sh

Make sure that the folder contains either only adsorbed state PDBs (and native.pdb) or solution state PDBs. Also make sure that all post processing scripts (found in the scripts/post_processing directory) are present in this directory as well

These commands will extract the top 4 adsorbed-state decoys for analysis and generate secondary structure, protein-protein contact maps, and protein-surface contact maps

Example output

  • Ads_SecStruct.png = adsorbed state secondary structure
  • Sol_SecStruct.png = solution state secondary struccture
  • Ads_ContactMap = adsorbed state contact map
  • Sol_ContactMap = solution state contact map
  • Surface_ContactMap.png = protein-surface contact map
  • Diff_ContactMap.png = difference map between contacts in the ads/sol state
  • lk_alpha_docked_to_calcite_0001.pdb = output final decoy
  • score.sc = scorefile
  • SolState_lk_alpha_docked_to_calcite_0001.pdb = solution state pdb
  • Surface_lk_alpha_docked_to_calcite_0001.pdb = adsorbed state pdb

Limitations

This app requires a single protein positioned above a solid surface whose parameters are present in Rosetta. The protein needs to appear before the surface in the pdb file and the two need to be separate chains