IRECS Documentation

Example Output

A test prediction has been run on the Glur2 receptor (PDB ID: 1m5d) with a target rotamer density of 2. That means that IRECS assigns on average two conformations two each side chain. The less constrained and the more flexible a side chain is, the more conformations it receives.

Both pictures visualize some part of the predicted protein. The crystal structure is colored in blue as a reference, the predicted side-chain conformations are colored according to their effective energy. Occupancy values for ambiguous atom positions are calculated from this energy with the Boltzmann law. Pictures were made using PyMOL


Tyrosine 61 to Glycine 73. The sequence of the displayed segment is YGARDADTKIWNG.	Lysine 258. IRECS assigns seven conformations to it, the correct conformation has the lowest effective energy and the highest occupancy

Below you see an excerpt of the IRECS output in PDB format. The temperature field holds the computed effective energy of the whole rotamer

ATOM 2034 NZ ALYS A 258 20.163 6.908 6.108 0.12 3.62 ATOM 2034 NZ BLYS A 258 19.258 8.880 6.451 0.17 2.64 ATOM 2034 NZ CLYS A 258 18.941 7.828 4.182 0.11 3.80 ATOM 2034 NZ DLYS A 258 18.931 7.681 4.305 0.14 3.14 ATOM 2034 NZ ELYS A 258 18.924 6.162 2.692 0.17 2.76 ATOM 2034 NZ FLYS A 258 20.109 5.582 4.261 0.15 2.98 ATOM 2034 NZ GLYS A 258 19.193 8.869 3.551 0.14 3.19

Installation

Usage

After installation, run the program with the help option '-h'. You should then see a screen similar to this:

hartmann@mpiat3300:~$ irecs -h Reading configuration file /TL/usr1/hartmann/IRECS/predict/config.irecs.txt USAGE (self-backbone mode): irecs -b template_file [OPTIONS] OR (mutation mode) : irecs -b template_file -m AnoA:_ [OPTIONS] OR (sequence mode) : irecs -b template_file -s sequence_file [OPTIONS] OPTIONS: -b, --template FILE set template pdb file -c, --config FILE set configuration file -d, --density NUM set rotamer density (default=1.0) -h, --help print this help screen -m, --mut AnoA:C mutate AA on chain C e.g. G21C:A -r, --ref FILE set reference pdb file -s, --sequence FILE set sequence file [fasta] -o, --output FILE set output pdb file Please report bugs to irecs@mpi-inf.mpg.de

Please note that the target sequence must have the same number of characters as the template has residues. Since IRECS does not model the target backbone, every gap character in the target sequence will be interpreted as a mutation to glycine.

Test run

You can see a test run of IRECS below. The protein 1M5D (PDB ID) can be found in the IRECS package.

hartmann@mpiat3300:~/IRECS/packages/common$ irecs -b 1m5d.pdb -r 1m5d.pdb -o 1m5d.irecs.pdb Reading configuration file /TL/usr1/hartmann/IRECS/predict/config.irecs.txt Reading charmm topology file /TL/usr1/hartmann/IRECS/predict/chem_data/charmm.all27.topology ... Reading binary BBDEP file /TL/usr1/hartmann/IRECS/predict/chem_data/bbdep.bin Reading atom pair potentials file /TL/usr1/hartmann/IRECS/predict/chem_data/sapdf.1_0.txt Reading template structure file 1m5d.pdb ... template structure 1m5d has 2 chains, 587 residues and 2366 atoms. Reference side-chain conformations found for 217 side-chains out of 217. Prediction on self backbone ... Rebuilding side chains ... ... 217 side chains have been rebuild. ... created 4954 conformations ... found 5551 neighbour residue pairs ... excluded 17885 distant residue pairs Scoring rotamer <-> backbone interactions ... ... filtered out 1757 rotamers. Scoring rotamer <-> rotamer interactions ... ... found 352271 conformation neighbours Starting IRECS algorithm ... Target rotamer density: 1 ---------------------------------------------------------- Iter Iter Res #native %native Rotamer total delta gone left left left left density energy energy ---------------------------------------------------------- 0 2977 217 217 100.00 14.72 1492.61 -0.37 2110 867 175 216 99.54 5.00 805.12 -1.94 2168 809 171 215 99.08 4.73 780.35 -0.95 2172 805 171 214 98.62 4.71 778.23 -0.91 2183 794 168 213 98.16 4.66 770.14 -0.66 2262 715 164 212 97.70 4.29 741.75 -0.43 2297 680 159 211 97.24 4.13 727.54 -0.13 2501 476 138 210 96.77 3.19 658.55 -1.22 2642 335 124 209 96.31 2.54 613.34 -0.32 2657 320 121 208 95.85 2.47 608.11 -0.94 2670 307 120 207 95.39 2.41 603.75 -0.18 2688 289 117 206 94.93 2.33 598.06 -0.86 2810 167 95 205 94.47 1.77 562.03 -0.57 2866 111 72 204 94.01 1.51 543.96 -0.42 2871 106 72 203 93.55 1.49 543.15 -0.26 2881 96 67 202 93.09 1.44 540.40 -0.37 2888 89 66 201 92.63 1.41 539.09 -0.14 2903 74 59 200 92.17 1.34 535.90 -0.21 2912 65 53 199 91.71 1.30 534.07 -0.26 2918 59 49 198 91.24 1.27 532.89 -0.24 2927 50 43 197 90.78 1.23 531.32 -0.22 2929 48 42 196 90.32 1.22 530.84 -0.12 2931 46 40 195 89.86 1.21 530.41 -0.21 2953 24 21 194 89.40 1.11 526.68 -0.14 2959 18 16 193 88.94 1.08 525.92 -0.12 2960 17 15 192 88.48 1.08 525.80 -0.12 2967 10 9 191 88.02 1.05 525.15 -0.08 2968 9 8 190 87.56 1.04 525.09 -0.06 2977 0 0 190 87.56 1.00 524.89 -0.01 ---------------------------------------------------------- Writing predicted structure to file 1m5d.irecs.pdb