Documentation
The documentation is incomplete. Please check again later for more detail.
Details and performance of the method are described in the following articles. Please cite these original papers when using results from this server:
- Sivasubramanian, A., Sicar, A., Chaudhury, S. & Gray, J.J. "High-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking". (submitted)
- Sivasubramanian, A., Maynard, J. A. & Gray, J.J. "Modeling the structure of mAb 14B7 bound to the anthrax protective antigen". Proteins, vol. 70. 1 (2008). pp. 218-230. Online | PDF
- A. Sivasubramanian, G. Chao, H.M. Pressler, K.D. Witrup, and J.J. Gray. "Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis." Structure, vol. 14. 3(2006). pp.401-414. Online | PDF
Protocol
Flowchart for RosettaAntibody homology modeling protocol
BLAST alignment terminology
Bit score
The value S' is derived from the raw alignment score S in which the statistical properties of the scoring system used have been taken into account. Because bit scores have been normalized with respect to the scoring system, they can be used to compare alignment scores from different searches.
Raw Score
The score of an alignment, S, calculated as the sum of substitution and gap scores. Substitution scores are given by a look-up table (see PAM, BLOSUM). Gap scores are typically calculated as the sum of G, the gap opening penalty and L, the gap extension penalty. For a gap of length n, the gap cost would be G+Ln. The choice of gap costs, G and L is empirical, but it is customary to choose a high value for G (10-15)and a low value for L (1-2).
BLOSUM
Blocks Substitution Matrix. A substitution matrix in which scores for each position are derived from observations of the frequencies of substitutions in blocks of local alignments in related proteins. Each matrix is tailored to a particular evolutionary distance. In the BLOSUM62 matrix, for example, the alignment from which scores were derived was created using sequences sharing no more than 62% identity. Sequences more identical than 62% are represented by a single sequence in the alignment so as to avoid over-weighting closely related family members. (Henikoff and Henikoff)
E value
Expectation value. The number of different alignents with scores equivalent to or better than S that are expected to occur in a database search by chance. The lower the E value, the more significant the score.
gap
A space introduced into an alignment to compensate for insertions and deletions in one sequence relative to another. To prevent the accumulation of too many gaps in an alignment, introduction of a gap causes the deduction of a fixed amount (the gap score) from the alignment score. Extension of the gap to encompass additional nucleotides or amino acid is also penalized in the scoring of an alignment.
Similarity
The extent to which nucleotide or protein sequences are related. The extent of similarity between two sequences can be based on percent sequence identity and/or conservation. In BLAST similarity refers to a positive matrix score.
PDB file structure (mostly from RosettaDock)
Atom coordinates
ATOM 1 N MET L 4 -15.197 35.942 2.724 1.00 0.00 ATOM 2 CA MET L 4 -14.079 35.887 3.650 1.00 0.00 ATOM 3 C MET L 4 -13.018 35.045 3.006 1.00 0.00 ATOM 4 O MET L 4 -13.330 34.005 2.426 1.00 0.00 ATOM 5 CB MET L 4 -14.492 35.189 4.942 1.00 0.00 ATOM 6 CG MET L 4 -13.330 34.946 5.913 1.00 0.00 ATOM 7 SD MET L 4 -13.650 33.611 7.170 1.00 0.00 ATOM 8 CE MET L 4 -14.586 34.554 8.356 1.00 0.00 ATOM 9 H MET L 4 -16.021 36.468 2.978 1.00 0.00 ATOM 10 HA MET L 4 -13.679 36.888 3.809 1.00 0.00 ATOM 11 1HB MET L 4 -15.243 35.818 5.416 1.00 0.00 ...
Summary
| score: | the total score using the all-atom (high-resolution) energy function (lower is better) |
| bk_tot: | total score used in the side-chain packing algorithm |
| fa_atr: | attractive portion of the lennard-jones potential (rewards close contacts) |
| fa_rep: | lennard-jones repulsive (penalizes overlaps) |
| fa_sol: | lazaridis-karplus solvation model (penalizes buried polars) |
| gsolt: | surface-area based solvation model |
| fa_dun: | internal energy of side chain rotamers as derived from dunbrack's statistics |
| fa_intrares: | intra-residue clashes |
| fa_pair: | statistics based pair term, favors salt bridges |
| 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 |
ntrials: 1
%accepted: 0.00
rms: 207.75
maxsub: nalign: 212 rms: 0.19 log_Evalue: -26.86
%_nat_cont: 0.89
rms_to_start: 8.52461994E-08
score: -463.00
env: -56.50 env_weight: 0
pair: -20.18 pair_weight: 0
vdw: 1.84 vdw_weight: 0
hs: 0.00 hs_weight: 0
ss: -96.13 ss_weight: 0
sheet: 10.07 sheet_weight: 0
r-sigma: -64.89 r-sigma_weight: 0
cb: 77.17 cb_weight: 0
rg: 17.63 rg_weight: 0
co: 44.13 co_weight: 0
contact_pred: 0.00 contact_weight: 0
rama: 19.27 rama_weight: 0.2
hb_srbb: -36.73 hb_srbb_weight: 0.5
hb_lrbb: -118.27 hb_lrbb_weight: 1
bk_tot: -511.19
fa_atr: -758.29
fa_rep: 47.32
fa_sol: 372.03
fa_h2o_sol: 0.00
fa_dun: 144.08
fa_intrares: 0.20
fa_pair: -27.94
gb_elec: 0.00
fa_plane: 0.00
fa_prob: -51.94
fa_h2o: 0.00
fa_h2o_hb: 0.00
fa_ref: 35.40
gsolt: 324.70
sasa: 23135.74
hb_sc: -46.26
sasapack: -0.26
Table of residue-specific energies
| Eatr: | lennard-jones attractive |
| Erep: | lennard-jones repulsive |
| Esol: | lazaridis-karplus solvation energy |
| Eh2o_sol: | solvation using explicit water, in default mode (not used) |
| Eaa_phipsi: | prob of an aa given phi and psi (not used) |
| Edun: | 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 (not used) |
| Eh2o, Eh2o_hb: | energies from explicit waters (not used) |
| Ecst: | constraint energies (not used) |
| Eres: | total for that residue (lower is better) |
res aa Eatr Erep Esol Eh2o_sol Eaa Edun Eintra Ehbnd_bb Ehbnd_sc Epair Eref Egb Eh2o Eh2o_hb Ecst Eres 4 MET -3.5 0.2 1.3 0.0 0.0 1.4 0.0 0.0 0.0 0.0 0.3 0.0 0.0 0.0 0.0 -1.0 5 THR -1.8 0.1 1.1 0.0 0.1 0.1 0.0 -1.2 0.0 0.0 0.3 0.0 0.0 0.0 0.0 -1.8 6 GLN -5.2 0.5 4.3 0.0 0.1 1.2 0.0 0.0 -1.2 -0.1 1.0 0.0 0.0 0.0 0.0 -1.3 7 THR -2.2 0.3 1.3 0.0 -0.3 0.4 0.0 -1.4 0.0 -0.1 0.3 0.0 0.0 0.0 0.0 -2.3 8 PRO -2.6 0.3 1.1 0.0 0.3 0.0 0.0 0.0 -0.4 0.0 0.0 0.0 0.0 0.0 0.0 -1.3 9 LEU -1.9 0.1 1.1 0.0 -0.2 0.4 0.0 -0.8 0.0 0.0 0.1 0.0 0.0 0.0 0.0 -1.3 10 SER -1.8 0.0 1.0 0.0 0.2 0.5 0.0 0.0 0.0 -0.1 0.4 0.0 0.0 0.0 0.0 -0.6 11 LEU -3.9 0.4 0.9 0.0 0.1 0.6 0.0 -1.4 0.0 0.0 0.1 0.0 0.0 0.0 0.0 -3.3 12 PRO -1.5 0.4 0.4 0.0 -0.5 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -0.8 13 VAL -2.5 0.3 0.7 0.0 0.2 0.1 0.0 -0.6 0.0 0.0 -0.3 0.0 0.0 0.0 0.0 -1.5 ...
Table of measured - expected energy
Measured - expected energy value is useful for determining how well packed a residue is. (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.) 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.
| Eatr: | lennard-jones attractive |
| Erep: | lennard-jones repulsive |
| Esol: | Lazaridis-Karplus solvation |
| Eaa_phipsi: | P(aa|phi,psi) |
| Edun: | 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. |
energies-average(in pdb) energies, AND rsd SASA packing score res chain aa nb Eatr Erep Esol Eaa Edun Eintra Ehbnd Epair Elj Eres SASApack res_rms sasaprob 4 L MET 22 1.1 -0.2 -0.5 0.1 -1.0 -0.1 1.0 0.0 0.9 -0.1 2.68 36.44 0.363 5 L THR 13 0.8 -0.1 -0.6 0.3 -0.4 0.0 -0.6 0.1 0.7 -0.4 4.92 34.61 0.155 6 L GLN 22 -0.3 0.2 0.9 0.2 -1.0 0.0 0.3 0.1 -0.1 0.0 6.21 33.74 0.241 7 L THR 15 0.6 0.1 -0.5 -0.2 -0.2 0.0 -0.6 0.0 0.7 -0.6 -1.82 31.89 0.696 8 L PRO 13 -0.2 -0.1 0.1 1.0 -0.6 0.0 -0.1 0.0 -0.3 0.2 -3.09 30.74 0.860 9 L LEU 12 0.8 -0.1 -0.1 -0.1 -0.9 -0.1 -0.2 0.0 0.6 -1.2 3.68 31.13 0.239 10 L SER 12 0.3 -0.2 -0.4 0.3 -0.4 0.0 0.6 0.0 0.1 0.4 6.47 29.63 0.106 ...
Measured - expected energies in different environments
actual-average(in pdb) energies per residue
Eatr Erep Elj
buried 0.0 0.0 -0.1
middle 0.1 -0.1 0.1
surfac 0.2 -0.1 0.1
Difference of chi angle (not used)
decoy chi angles - starting chi angles res aa chi1 chi2 chi3 chi4 4 MET 0.00 0.00 0.00 0.00 chi_offsets 5 THR 0.00 0.00 0.00 0.00 chi_offsets 6 GLN 0.00 0.00 0.00 0.00 chi_offsets 7 THR 0.00 0.00 0.00 0.00 chi_offsets 8 PRO 0.00 0.00 0.00 0.00 chi_offsets ...
Absolute decoy chi angles
absolute decoy chi angles res aa chi1 chi2 chi3 chi4 4 MET 173.455 -159.410 -81.934 0.000 2 2 3 0 chi_absolute 5 THR -58.550 -60.000 0.000 0.000 3 0 0 0 chi_absolute 6 GLN -176.834 176.088 -22.320 0.000 2 2 3 0 chi_absolute 7 THR 59.568 180.000 0.000 0.000 1 0 0 0 chi_absolute 8 PRO 34.964 0.000 0.000 0.000 1 0 0 0 chi_absolute ...
Miscellaneous
| res: | Sequential residue number, does not match the one in pdb files |
| ss: | Secondary structure (L: loop, E: strand, H: helix) |
| frag | Fragments (INPT: input, -SH-: modified by shear moves, -SM-: modified by small moves) |
complete: res ss phi psi omega frag rama seq dstart_tor dnat_tor ... 94 E -67.876 151.961 -176.253 INPT -1.10 R 0.000 167.505 95 L -141.153 115.573 179.817 -SH- 1.51 W 0.000 333.014 96 E -143.038 -138.702 177.913 -SM- 4.38 G 0.000 449.991 97 L -54.728 -25.570 -173.750 -SH- -0.45 S 0.000 200.802 98 L -97.591 3.749 -149.708 -SM- -0.96 Y 0.000 113.432 99 L 47.139 -127.452 -166.108 -SM- 9.28 A 0.000 275.455 100 L -91.502 72.678 -167.819 -SH- 0.69 M 0.000 234.624 101 L -80.957 -28.905 174.097 -SM- -0.86 D 0.000 179.434 102 L -120.436 144.341 -179.498 -SH- -0.77 Y 0.000 247.626 103 L -131.996 150.399 173.932 -SM- -0.32 W 0.000 163.917 104 L -78.010 -179.619 -176.175 INPT -0.32 G 0.000 9.311 ...