Author: Chu Wang; transcribed by Steven Lewis (smlewi@gmail.com)

The transcription into the doc folder was performed 6/18/12 by Steven Lewis. It is known that this documentation is not yet "up to spec".

Protocols for the metalloprotein abrelax application are based on standard protein folding and loop modeling protocols (see documentation for the abinitio-relax application) with additional constraint files.

In addition to the input files required for abinitio relax, the following input files are required to run this application:

1. fasta file – This file contains the protein sequence to be modeled. The sequence required for this application must be more annotated than the standard one with [CYZ] or [HIS] to mark the residues that chelate the zinc, and Z[ZN] at the end for extra "zinc" residue.

2. residue_pair_jump_cst – explanation after ##

BEGIN  ## starting marker
jump_def: 3 60 59 59
## a rigid-body jump from the residue 3(first zinc-chelating residue) to 60(zinc) with a cut point starting at 59 and ending at 59 (last protein residue) This is to define how the fold tree is generated.
aa: CYS ZN
## the residues on both sides of the jump
cst_atoms: SG CB CA ZN V1 V2
## how distance, angular and dihedral parameters are defined
jump_atoms: C CA N ZN V1 V2
## how the jump is defined between in the atom tree
disAB: 2.20
angleA: 68.0
angleB: 70.5
dihedralA: -150.0 -120.0 -90.0 -60.0 -30.0 0.0 30.0 60.0 90.0 120.0 150.0 180.0
dihedralAB: -150.0 -120.0 -90.0 -60.0 -30.0 0.0 30.0 60.0 90.0 120.0 150.0 180.0
dihedralB: 120.0
## all the degrees of freedom as defined in Figure 1 and Table 1 to generate various jump transformations between CYS and ZN
END ## ending marker

each blocks as above can define one zinc binding site and if you have more than one zinc, append more blocks like this.

3. cen_cst or fa_cst files: These files are used to define constraints to keep chelating geometry optimal between zinc and other three chelating residues. The files are in standard Rosetta distance and angular constraints format (see the constraint file documentation).

For examples of metalloprotein-abrelax input files, please check the integration test input. Integration tests for the metalloprotein_abrelax application are located in the following directory:

main/test/integration/tests/metalloprotein_abrelax/

All necessary input files for these integration tests can be found in:

main/test/integration/tests/metalloprotein_abrelax/input/