• Interpreting your results
• Tendencies
• File formats
• FAQ
• Related papers

Interpreting your results:

1. Interpreting your results from RosettaDesign: 

The energies, structure and sequence output by RosettaDesign are placed in 
a pdb file.  

The pdb file has the following sections:

1) coordinates of the design structure

2) a list of scores.  Many of these scores are used in ab initio structure prediction and are not particularly
   relevant to protein design.  The scores used during design with the default protocols are:

   total: the total score using the design energy function (lower is better)
   LJatr: attractive portion of the lennard-jones potential (rewards close contacts)
   LJrep: lennard-jones repulsive (penalizes overlaps)
   LKsol: lazaridis-karplus solvation model (penalizes buried polars)
   Erot: internal energy of side chain rotamers as derived from dunbrack's statistics
   Eintra: intra-residue clashes
   Epair: statistics based pair term, favors salt bridges
   Eaa_phipsi: P(aa|phi,psi), ramachandran preferences
   hb_sc: sidechain-sidechain and sidechain-backbone hydrogen bond energy
   hb_srbb: backbone-backbone hbonds close in primary sequence
   hb_lrbb: backbone-backbone hbonds distant in primary sequence   


3) a table of energies for each residue in the protein: totals are at the 
   bottom

   LJatr: lennard-jones attractive
   LJrep: lennard-jones repulsive
   LKsol: lazaridis-karplus solvation energy
   Eh2o_sol: solvation using explicit water, in default mode this is not used
   Eaa_phipsi: prob of an aa given phi and psi
   Erot: rotamer internal energies
   Eintra: internal clashes within residues
   Ehbnd: total hydrogen bonding per residue
   Epair: pair probabilities derived from the pdb database
   Eref: reference energy for each amino acid
   Egb: generalized born solvation energy, in default mode this is not used
   Eh2o, Eh2o_hb: energies from explicit waters
   Ecst: constraint energies
   Eres: total for that residue (lower is better)

example of residue energy table:
res aa    LJatr     LJrep   LKsol  Eh2o_sol Eaa_phipsi  Erot  Eintra    Ehbnd   Epair   Eref   Egb  Eh2o  Eh2o_hb  Ecst   Eres
  1 MET    -4.0     0.3     1.4     0.0       0.0       2.5     0.3     -0.8     0.0     0.3   0.0   0.0    0.0     0.0   -0.7
  2 GLN    -2.5     0.1     1.5     0.0       0.0       2.9     0.0     -0.7    -0.1     1.0   0.0   0.0    0.0     0.0    0.3
  3 ILE    -4.1     0.1     1.2     0.0      -0.2       0.1     0.4     -1.6     0.0    -0.2   0.0   0.0    0.0     0.0   -3.9
  4 PHE    -4.4     0.5     1.8     0.0      -0.3       0.2     0.0     -1.6     0.0    -0.6   0.0   0.0    0.0     0.0   -3.2
  5 THR    -3.5     0.0     1.8     0.0       0.0       0.0     0.0     -1.4     0.0     0.3   0.0   0.0    0.0     0.0   -3.3
  6 LYS    -3.0     0.0     1.5     0.0       0.1       0.9     0.1     -1.7     0.0     0.6   0.0   0.0    0.0     0.0   -2.8
  7 THR    -3.1     0.1     1.9     0.0      -0.7       0.3     0.0     -1.2     0.0     0.3   0.0   0.0    0.0     0.0   -3.0
  8 LEU    -1.3     0.0     0.5     0.0       0.0       1.6     0.5      0.0     0.0     0.1   0.0   0.0    0.0     0.0    1.2
  9 THR    -1.4     0.1     1.1     0.0      -0.1       0.8     0.0     -0.2     0.0     0.3   0.0   0.0    0.0     0.0    0.1
 10 GLY    -0.8     0.1     0.6     0.0      -1.5      -0.0     0.0     -0.3     0.0     0.2   0.0   0.0    0.0     0.0   -2.2
 11 LYS    -2.8     0.1     2.4     0.0       0.0       4.4     0.2     -0.7    -0.3     0.6   0.0   0.0    0.0     0.0    2.6


4) a table of: measured energies - expected energies (expected energies are derived
    by calculating the average energies of the different amino acids with a certain
    number of neighbors in a large set of proteins in the pdb)
    This table is useful for determining how well packed a residue is.  The column Elj
    compares the actual lennard jones energy of residue to the expected value.  Well 
    packed residues should have Elj scores new zero or negative. 

    LJatr: lennard-jones attractive
    LJrep: lennard-jones repulsive
    LKsol: Lazaridis-Karplus solvation
    Eaa_phipsi: P(aa|phi,psi)
    Erot: rotamer preferences from dunbrack's library
    Eintra: intra residue clashes
    Ehbnd: hydrogen bonding
    Epair: statistics based pair term
    Elj: lennard-jones total 
    Eres: total per residue
    SASApack: SASApack is related to the void volume in a protein. Surface areas are computed with 
        a 1.4 angstrom probe and 0.5 angstrom probe and the difference (ASA_0.5 - ASA_1.4) is compared
	to the expected difference for a particular residue type in a particular environment.  A negative
        value is favorable and indicates that the residue is more tightly packed than is seen in average 
        pdb files.  

example:
energies-average(in pdb) energies, AND rsd SASA packing score
res  aa nb   LJatr    LJrep   LKsol  Eaa_phipsi  Erot  Eintra  Ehbnd  Epair  Elj     Eres SASApack
  1 MET 15    -0.8    -0.1     0.0     0.0       -0.2   0.2    -0.1    0.0   -1.0    -1.7     2.38
  2 GLN 11     0.2    -0.2    -0.3     0.1        0.3   0.0    -0.1    0.0    0.0    -0.4     8.93
  3 ILE 22     0.3    -0.2    -0.3     0.0       -1.2   0.4    -0.6    0.0    0.1    -1.8    18.02
  4 PHE 14    -0.3     0.1     0.4    -0.2       -1.0  -0.1    -1.0    0.0   -0.2    -2.5     1.89
  5 THR 22     0.2    -0.3    -0.5     0.1       -0.5   0.0    -0.3    0.1    0.0    -1.0    11.62
  6 LYS 15     0.3    -0.4    -0.5     0.1       -2.2   0.1    -0.9    0.2   -0.1    -3.6     5.48
  7 THR 18     0.1    -0.2    -0.2    -0.6       -0.3   0.0    -0.2    0.1   -0.1    -1.1    10.38
  8 LEU 10     0.9    -0.2    -0.6     0.1        0.1   0.5     0.5    0.0    0.8     0.9     1.33


5) a table of, total measured energies - expected energies, for residues in different 
   environments: surface, buried and exposed.  When creating novel structures we have found it difficult 
   to get Elj numbers that are zero or negative for the buried residues.

example:
actual-average(in pdb) energies per residue
       LJatr   LJrep   Elj
buried  -0.1   -0.2   -0.3
middle  -0.3   -0.1   -0.3
surfac   0.1   -0.1    0.0


6) a table of starting minus finishing chi angles, and absolute chi angles

7) phi, psi and omega angle for each residue

Tendencies:

RosettaDesign Tendencies
In some cases RosettaDesign does appear to make odd choices, and it helps
to know beforehand what some of these tendencies are.  In these situations it
is probably best to use a resfile to try and point Rosetta away from these
pitfalls.


1) The program likes to put amino acids with similar chemical properties near each other. 
This is primarily because polar residues can hydrogen bond with each other, and hydrophobics 
can pack without burying hbonding groups. The result is that in some cases you may observe a 
large cluster of hydrophobic residues on the surface of a protein, or a cluster of polars in 
the core. In some cases this can be avoided by forcing key residues to be polar or hydrophobic.

2) Sometimes polar groups are buried without a hydrogen bonding partner. The
energy function has been parameterized to try and avoid this, but there is
no filter that prevents it.

File formats:
PDB file format description:

Please go to PDB Format Description for more details.
Record Format:
COLUMNS        DATA TYPE       FIELD         DEFINITION
---------------------------------------------------------------------------------
 1 -  6        Record name     "ATOM  "

 7 - 11        Integer         serial        Atom serial number.

13 - 16        Atom            name          Atom name.

17             Character       altLoc        Alternate location indicator.
18 - 20        Residue name    resName       Residue name.

22             Character       chainID       Chain identifier.

23 - 26        Integer         resSeq        Residue sequence number.

27             AChar           iCode         Code for insertion of residues.

31 - 38        Real(8.3)       x             Orthogonal coordinates for X in
                                             Angstroms.

39 - 46        Real(8.3)       y             Orthogonal coordinates for Y in
                                             Angstroms.

47 - 54        Real(8.3)       z             Orthogonal coordinates for Z in
                                             Angstroms.

55 - 60        Real(6.2)       occupancy     Occupancy.

61 - 66        Real(6.2)       tempFactor    Temperature factor.

73 - 76        LString(4)      segID         Segment identifier, left-justified.

77 - 78        LString(2)      element       Element symbol, right-justified.

79 - 80        LString(2)      charge        Charge on the atom.

This file specifies which residues will be varied

 Column   2:    Chain
 Column   4-7:  sequential residue number
 Column   9-12: pdb residue number
 Column  14-18: id  (described below)
 Column  20-40: amino acids to be used

 NATAA  => use native amino acid
 ALLAA  => all amino acids
 NATRO  => native amino acid and rotamer
 PIKAA  => select individual amino acids
 POLAR  => polar amino acids
 APOLA  => apolar amino acids

 The following demo lines are in the proper format

 A    1    3 NATAA
 A    2    4 ALLAA
 A    3    6 NATRO
 A    4    7 NATAA
 B    5    1 PIKAA  DFLM
 B    6    2 PIKAA  HIL
 B    7    3 POLAR
 -------------------------------------------------
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