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Browser compatibility

OS Version Chrome Firefox Microsoft Edge Safari
Windows 10 22H2 108.0.5359.99 n/a 108.0.1462.46 n/a
macOS 10.15.7 (Catalina) 108.0.5359.99 107.0, 108.0, 108.0.1 not tested 15.6.1
Linux Ubuntu 20.04 108.0.5359 107.0 n/a n/a
Linux Ubuntu 22.04 1:85.0.4183.83 108.0 n/a n/a

Minimization

A short molecular dynamics simulation is performed for the top predicted poses in order to relax interactions and removing atomic clashes.

The protocol is performed by the OpenMM framework in the following conditions:

forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=CutoffNonPeriodic, nonbondedCutoff=0.5*nanometer, constraints=HBonds)
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
simulation = Simulation(pdb.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.minimizeEnergy()
simulation.step(100)

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PDB support

Depending on molecule type, only specific residue or nucleotides might be supported. This also includes specific atom type names. Please find a detailed list of atomic instances compatible with the LightDock Server.

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DFIRE scoring function

DFIRE statistical potential has only support for standard residue types and protonation (hydrogen atoms) are simply removed. A new artificial bead called MMB-BJ is added to the force-field to support fake lipidic membrane boundaries.

Residue Name Atom types
ALAN CA C O CB
CYSN CA C O CB SG
ASPN CA C O CB CG OD1 OD2
GLUN CA C O CB CG CD OE1 OE2
PHEN CA C O CB CG CD1 CD2 CE1 CE2 CZ
GLYN CA C O
HISN CA C O CB CG ND1 CD2 CE1 NE2
ILEN CA C O CB CG1 CG2 CD1
LYSN CA C O CB CG CD CE NZ
LEUN CA C O CB CG CD1 CD2
METN CA C O CB CG SD CE
ASNN CA C O CB CG OD1 ND2
PRON CA C O CB CG CD
GLNN CA C O CB CG CD OE1 NE2
ARGN CA C O CB CG CD NE CZ NH1 NH2
SERN CA C O CB OG
THRN CA C O CB OG1 CG2
VALN CA C O CB CG1 CG2
TRPN CA C O CB CG CD1 CD2 CE2 NE1 CE3 CZ3 CH2 CZ2
TYRN CA C O CB CG CD1 CD2 CE1 CE2 CZ OH
MMBBJ

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Protein-Nucleic

Protein-Nucleic scoring function is based on the AMBER94FF types. Protonation is automatically calculated by Reduce software (user input protonation status is removed). Some translation between atom types is required, e.g. OP1 to O1P, and it is automatically performed by the server.

List of supported nucleotides and atom types is detailed below:

Nucleotide Atom types
DAP, O1P, O2P, O5', C5', H5'1, H5'2, C4', H4', O4', C1', H1', N9, C8, H8, N7, C5, C6, N6, H61, H62, N1, C2, H2, N3, C4, C3', H3', C2', H2'1, H2'2, O3'
DCP, O1P, O2P, O5', C5', H5'1, H5'2, C4', H4', O4', C1', H1', N1, C6, H6, C5, H5, C4, N4, H41, H42, N3, C2, O2, C3', H3', C2', H2'1, H2'2, O3'
DGP, O1P, O2P, O5', C5', H5'1, H5'2, C4', H4', O4', C1', H1', N9, C8, H8, N7, C5, C6, O6, N1, H1, C2, N2, H21, H22, N3, C4, C3', H3', C2', H2'1, H2'2, O3'
DTP, O1P, O2P, O5', C5', H5'1, H5'2, C4', H4', O4', C1', H1', N1, C6, H6, C5, C7, H71, H72, H73, C4, O4, N3, H3, C2, O2, C3', H3', C2', H2'1, H2'2, O3'
AP, O1P, O2P, O5', C5', H5'1, H5'2, C4', H4', O4', C1', H1', N9, C8, H8, N7, C5, C6, N6, H61, H62, N1, C2, H2, N3, C4, C3', H3', C2', H2'1, O2', HO'2, O3'
CP, O1P, O2P, O5', C5', H5'1, H5'2, C4', H4', O4', C1', H1', N1, C6, H6, C5, H5, C4, N4, H41, H42, N3, C2, O2, C3', H3', C2', H2'1, O2', HO'2, O3'
GP, O1P, O2P, O5', C5', H5'1, H5'2, C4', H4', O4', C1', H1', N9, C8, H8, N7, C5, C6, O6, N1, H1, C2, N2, H21, H22, N3, C4, C3', H3', C2', H2'1, O2', HO'2, O3'
UP, O1P, O2P, O5', C5', H5'1, H5'2, C4', H4', O4', C1', H1', N1, C6, H6, C5, H5, C4, O4, N3, H3, C2, O2, C3', H3', C2', H2'1, O2', HO'2, O3'

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Results

LightDock server provides a compressed file containing all relevant information provided and generated by the LightDock simulation, including the top 100 predicted poses by the selected protocol (top/ directory) in the PDB format.

An exhaustive list of files generated during the setup of the simulation can be found here.

All files generated by the LightDock Server and provided in the results page of the job follow the same standard and structure in terms of file format, reproducibility and repeatability of the results as described in the stand-alone version of the LightDock software. Please visit the Tutorials section of the LightDock official website for the most up-to-date information of the LightDock software, including a specific section on how to use this server.

Additionally, users may ask questions directly to the developers via the official Slack space.

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Server version

Software Version
LightDock0.9.3.post1
LightDock-Rust0.3.0

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Third-party software

We thank all the third-party software providers used by this server:

Software Version
PDBFixer1.8.1
OpenMM7.7
Reducereduce.4.9.210817

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Benchmarking & References

Please cite this reference if you use the LightDock-Server:

The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions
Brian Jiménez-García, Jorge Roel-Touris, Didier Barradas-Bautista
Nucleic Acids Research, 2023;, gkad327, doi: https://doi.org/10.1093/nar/gkad327


LightDock has been systematically validated against multiple publicly available datasets and its predictive performance reported in different publications. Please find below a list of all publications and links to public available data repositories:

Publications

Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking
Paulo C. T. Souza Gilberto P. Pereira, Brian Jiménez-García, Riccardo Pellarin, Guillaume Launay, Sangwook Wu, Juliette Martin
bioRxiv doi: https://doi.org/10.1101/2023.02.16.528819

Integrative Modeling of Membrane-associated Protein Assemblies
Jorge Roel-Touris, Brian Jiménez-García & Alexandre M.J.J. Bonvin
Nat Commun 11, 6210 (2020); doi: https://doi.org/10.1038/s41467-020-20076-5

LightDock goes information-driven
Jorge Roel-Touris, Alexandre M.J.J. Bonvin and Brian Jiménez-García
Bioinformatics, Volume 36, Issue 3, 1 February 2020, Pages 950–952, doi: https://doi.org/10.1093/bioinformatics/btz642

LightDock: a new multi-scale approach to protein–protein docking
Brian Jiménez-García, Jorge Roel-Touris, Miguel Romero-Durana, Miquel Vidal, Daniel Jiménez-González and Juan Fernández-Recio
Bioinformatics, Volume 34, Issue 1, 1 January 2018, Pages 49–55, doi: https://doi.org/10.1093/bioinformatics/btx555

Public available data repositories
Description Repository
Protein-protein Docking Benchmark 5 LightDock performance evaluated by DockQ https://github.com/lightdock/bm5
The performance of the residue restraint driven protocol evaluated on the new 55 cases of the protein-protein Docking Benchmark 5 https://github.com/lightdock/lightdock_bm5
Integrative Modeling of Membrane-associated Protein Assemblies: Dataset https://github.com/lightdock/membrane_docking
Restraints how-to and examples https://github.com/lightdock/test_restraints

LightDock is a FOSS project, all data and code is public and available at https://github.com/lightdock.

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