NPDock
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The exemplary output with explanations for the demo input can be found here.Input
NPDock accepts input files in the formats: (1) (old and new) PDB format (2) AMBER format (3) CHARMM format (4) mol2 format.Only lines starting with
ATOM are taken under consideration! If any heteroatoms should be taken under consideration during the docking process, change word HETATM to ATOM in the pdb file.
Check if your pdb files have NO more than 10000 atoms. This is a technical limitation due to the use of the GRAMM program.
If you have any problem with preparation of your file, let us know npdock@genesilico.pl
Examples of input files in the PDB format:
ATOM 1 N GLY A 1 1.275 -7.458 53.298 0.00 00.00 0
ATOM 2 CA GLY A 1 0.279 -6.475 52.757 0.00 00.00 0
ATOM 3 C GLY A 1 0.527 -5.062 53.261 0.00 00.00 0
ATOM 4 O GLY A 1 0.980 -4.877 54.400 0.00 00.00 0
ATOM 5 N HIS A 2 0.215 -4.062 52.426 0.00 00.00 0
[..]
ATOM 3926 O3' A B 400 8.073 -8.490 35.738 0.00 00.00 0 ATOM 3927 P A B 401 6.685 -8.781 35.311 0.00 00.00 0 ATOM 3928 OP1 A B 401 5.986 -9.380 36.472 0.00 00.00 0 ATOM 3929 OP2 A B 401 6.734 -9.558 34.051 0.00 00.00 0 ATOM 3930 O5' A B 401 5.979 -7.396 34.945 0.00 00.00 0 [..]
ATOM 1 P DG B 1 -0.356 9.218 1.848 1.00 0.00 P ATOM 2 OP1 DG B 1 -0.311 10.489 2.605 1.00 0.00 O ATOM 3 OP2 DG B 1 -1.334 9.156 0.740 1.00 0.00 O ATOM 4 O5' DG B 1 1.105 8.869 1.295 1.00 0.00 O ATOM 5 C5' DG B 1 2.021 8.156 2.146 1.00 0.00 C ATOM 6 C4' DG B 1 2.726 7.072 1.355 1.00 0.00 C [..]
Examples of input file in the AMBER format:
ATOM 4 O5' RU5 A 2 34.071 -4.485 -19.569 1.00 49.72 O ATOM 5 C5' RU5 A 2 35.075 -3.477 -19.544 1.00 48.99 C ATOM 6 C4' RU5 A 2 35.702 -3.343 -20.913 1.00 48.14 C ATOM 7 O4' RU5 A 2 36.266 -4.621 -21.311 1.00 48.31 O ATOM 8 C3' RU5 A 2 34.748 -2.995 -22.044 1.00 47.64 C ATOM 9 O3' RU5 A 2 34.611 -1.590 -22.118 1.00 48.11 O ATOM 10 C2' RU5 A 2 35.508 -3.506 -23.255 1.00 47.66 C ATOM 11 O2' RU5 A 2 36.552 -2.617 -23.597 1.00 49.84 O ATOM 12 C1' RU5 A 2 36.106 -4.803 -22.709 1.00 46.10 C ATOM 13 N1 RU5 A 2 35.254 -5.984 -22.920 1.00 40.05 N ATOM 14 C2 RU5 A 2 35.352 -6.656 -24.131 1.00 39.64 C ATOM 15 O RU5 A 2 36.102 -6.306 -25.034 1.00 41.63 O ATOM 16 N3 RU5 A 2 34.542 -7.755 -24.245 1.00 38.23 N ATOM 17 C4 RU5 A 2 33.667 -8.237 -23.300 1.00 37.45 C ATOM 18 O4 RU5 A 2 32.991 -9.225 -23.561 1.00 36.32 O ATOM 19 C5 RU5 A 2 33.620 -7.488 -22.083 1.00 35.99 C ATOM 20 C6 RU5 A 2 34.391 -6.414 -21.939 1.00 37.75 C ATOM 21 P RU A 3 33.246 -0.941 -22.655 1.00 48.41 P ATOM 22 O1P RU A 3 33.383 0.511 -22.367 1.00 47.45 O ATOM 23 O2P RU A 3 32.083 -1.692 -22.107 1.00 45.44 O1- [..]
Examples of input file in the CHARMM format:
ATOM 1 P GUA B 1 -0.356 9.218 1.848 1.00 0.00 ATOM 2 C5' GUA B 1 2.021 8.156 2.146 1.00 0.00 ATOM 3 O5' GUA B 1 1.105 8.869 1.295 1.00 0.00 ATOM 4 C4' GUA B 1 2.726 7.072 1.355 1.00 0.00 ATOM 5 O4' GUA B 1 1.986 5.817 1.352 1.00 0.00 ATOM 6 C3' GUA B 1 2.952 7.370 -0.127 1.00 0.00 ATOM 7 O3' GUA B 1 4.210 6.832 -0.518 1.00 0.00 ATOM 8 C2' GUA B 1 1.848 6.598 -0.850 1.00 0.00 ATOM 9 C1' GUA B 1 1.913 5.344 0.016 1.00 0.00 ATOM 10 N1 GUA B 1 0.233 0.533 0.025 1.00 0.00 ATOM 11 C2 GUA B 1 1.516 1.023 0.172 1.00 0.00 ATOM 12 N2 GUA B 1 2.476 0.111 0.344 1.00 0.00 ATOM 13 N3 GUA B 1 1.811 2.321 0.149 1.00 0.00 ATOM 14 C4 GUA B 1 0.709 3.095 -0.035 1.00 0.00 ATOM 15 C5 GUA B 1 -0.599 2.700 -0.190 1.00 0.00 ATOM 16 C6 GUA B 1 -0.914 1.317 -0.165 1.00 0.00 ATOM 17 O6 GUA B 1 -2.010 0.775 -0.284 1.00 0.00 ATOM 18 N7 GUA B 1 -1.430 3.807 -0.354 1.00 0.00 ATOM 19 C8 GUA B 1 -0.606 4.826 -0.294 1.00 0.00 [..]
Examples of input file in the mol2 format:
@<TRIPOS>MOLECULE
1xjr_clx.pdb
1005 1111 59 0 0
NUCLEIC_ACID
NO_CHARGES
@<TRIPOS>ATOM
1 P 68.0840 42.0920 40.7180 P.3 1 G 0.0000
2 OP1 67.0150 42.3730 41.6950 O.co2 1 G 0.0000
3 OP2 67.9370 40.8620 39.9050 O.co2 1 G 0.0000
4 O5' 68.1740 43.3640 39.7500 O.3 1 G 0.0000
5 C5' 67.8240 44.6880 40.1040 C.3 1 G 0.0000
[..]
Help
Job title – could be any string.
RNA-protein/DNA-protein - indication of the nucleic acid (DNA or RNA) that will be docked to the protein.
Protein - a pdb file with protein structure, only lines started from “ATOM” will be considered during the docking process. The pdb file description is available here.
RNA/DNA - a pdb file with RNA or DNA structure. DNA structure should have “D” in the one letter residue name (examples: DA, DG, DT or DC). Only lines started from “ATOM” will be considered during the docking process. The pdb file description is available here.
Optional parameters
Select chains
Chain Ids for the Protein - one or several letters that indicate chain id’s of downloaded protein. Separate chain id’s by comma without spaces. Example: A,B - chains A and B; C - chain C; * - all chains
Chain Ids for the RNA/DNA - one or several letters that indicate chain id’s of downloaded nucleic acid. Separate chain id’s by comma without spaces. Example: K,L - chains K and L; N - chain N; * - all chains
Interfaces filtering
Protein interface - protein interface residues. Example: 10-33:A,5:B,18:B indicate protein residues from 10 to 33 in chain A as well as residues 5 and 18 in chain B. * - all residues. Do not use spaces.
RNA/DNA interface - nucleic acid interface residues. Example: 1-15:K,10:L indicate nucleic acid residues from 1 to 15 in chain K and residue 10 in chain L. * - all residues. Do not us spaces.
Number residues of interfaces in contact - number of protein-nucleic acid residues pairs from the potential interface list that are required to be in contact. Must be at least 1, don't leave it empty.
Advanced optional parameters
Clustering procedure
Number of the best scored models used for clustering - less than 1000 is recommended.
RMSD cut-off for clustering [Ångström] - the highest RMSD between structures in the same cluster. Less than 10 is recommended.
Refinement with MC
Number of steps of simulation – numer of basic steps of the Monte Carlo simulation. Not all steps will be accepted! Not less than 1000 and not more than 10000 is recomended.
Temperature of the first step of simulation [in Kelvin] – this parameter is necessary for simulated annealing algorithm. Highest temperature allows for higher movement freedom.
Temperature of the last step of simulation [in Kelvin] – this parameter is necessary for the simulated annealing algorithm. We recommend not to change this parameter.
Every accepted step is saved – each accepted step of MC simulation is saved in the trajectory file. Please do not choose this parameter with highly increasing step number parameter and/or for really big molecules.
Lowest energy structure is saved every [ 10 ] step - it is better choice for very long simulations and/or big molecules