Metadata

Author: Andrea Bazzoli (ndrbzz [at] gmail.com)

Last updated: July 2017

Code

The application's code lives in src/apps/public/analysis/interface_energy.cc.

Application's purpose

Given two residue sets, or "faces", computes their interface energy as the sum of pairwise residue energies over all residue pairs (R1, R2), R1 belonging to face #1 and R2 belonging to face #2.

Usage

Command line

interface_energy -s <POSE> -face1 <FACE1> -face2 <FACE2> -score:hbond_bb_per_residue_energy

<FACE1> and <FACE2> are paths to two files that define face #1 and face #2, respectively. Each file specifies one residue per line by indicating—in that order—the residue's chain ID, sequence number, and insertion code in the input PDB file.

Input example

The following <FACE1> defines a face consisting of residues 58, 59, and 60 from chain H:

H 58 _
H 59 _
H 60 _

The following <FACE2> defines a face consisting of residues 94 and 95 from chain A:

A 94 _
A 95 _

Note that a blank insertion code is denoted by underscore (_).

Output (on screen)

Pairwise energies of all residue pairs (R1, R2) for each of several types of energy (short-ranged, context-dependent long-range, context-independent long-range).
Total interface energy, computed as the sum of those pairwise contributions.

For example, the output for the above two faces (given a certain input pose) is the following:

##### PAIRWISE SHORT-RANGE ENERGIES #####
ILE58_H(51) --- HIS94_A(220): 0
ILE58_H(51) --- PRO95_A(221): 0
ASN59_H(52) --- HIS94_A(220): 0
ASN59_H(52) --- PRO95_A(221): 0
TRP60_H(53) --- HIS94_A(220): -0.92086
TRP60_H(53) --- PRO95_A(221): -0.962562

##### PAIRWISE ENERGIES FOR CI_LR_2B METHOD IN CHARGE OF dslf_ss_dst #####
ILE58_H(51) --- HIS94_A(220): 0
ILE58_H(51) --- PRO95_A(221): 0
ASN59_H(52) --- HIS94_A(220): 0
ASN59_H(52) --- PRO95_A(221): 0
TRP60_H(53) --- HIS94_A(220): 0
TRP60_H(53) --- PRO95_A(221): 0

##### PAIRWISE ENERGIES FOR CI_LR_2B METHOD IN CHARGE OF rama_prepro #####
ILE58_H(51) --- HIS94_A(220): 0
ILE58_H(51) --- PRO95_A(221): 0
ASN59_H(52) --- HIS94_A(220): 0
ASN59_H(52) --- PRO95_A(221): 0
TRP60_H(53) --- HIS94_A(220): 0
TRP60_H(53) --- PRO95_A(221): 0

##### TOTAL INTERFACE ENERGY: -1.88342

In the notation used to specify a residue, after the obvious descriptors, the number in parentheses denotes the residue's index in the pose.

Note that energy types which are inactive, and hence contribute no energy (like context-dependent long-range energies in the above example), are not included in the output.

References

[1] Bazzoli A, Vance DJ, Rudolph MJ, Rong Y, Angalakurthi SK, Toth IV RT, Middaugh CR, Volkin DB, Weis DD, Karanicolas J, Mantis NJ. Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies. Proteins: Structure, Function, and Bioinformatics, doi: 10.1002/prot.25353, 2017.

interface_energy: energy at the interface between two sets of residues