|macOS||10.15.7 (Catalina)||108.0.5359.99||107.0, 108.0, 108.0.1||not tested||15.6.1|
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)
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.
If backbone flexibility is enabled, please make sure all provided residue and nucleotide have no missing backbone atoms. Otherwise ANM protocol might fail.
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|
|ALA||N CA C O CB|
|CYS||N CA C O CB SG|
|ASP||N CA C O CB CG OD1 OD2|
|GLU||N CA C O CB CG CD OE1 OE2|
|PHE||N CA C O CB CG CD1 CD2 CE1 CE2 CZ|
|GLY||N CA C O|
|HIS||N CA C O CB CG ND1 CD2 CE1 NE2|
|ILE||N CA C O CB CG1 CG2 CD1|
|LYS||N CA C O CB CG CD CE NZ|
|LEU||N CA C O CB CG CD1 CD2|
|MET||N CA C O CB CG SD CE|
|ASN||N CA C O CB CG OD1 ND2|
|PRO||N CA C O CB CG CD|
|GLN||N CA C O CB CG CD OE1 NE2|
|ARG||N CA C O CB CG CD NE CZ NH1 NH2|
|SER||N CA C O CB OG|
|THR||N CA C O CB OG1 CG2|
|VAL||N CA C O CB CG1 CG2|
|TRP||N CA C O CB CG CD1 CD2 CE2 NE1 CE3 CZ3 CH2 CZ2|
|TYR||N CA C O CB CG CD1 CD2 CE1 CE2 CZ OH|
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.
O1P, and it is automatically performed by the server.
List of supported nucleotides and atom types is detailed below:
|DA||P, 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'|
|DC||P, 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'|
|DG||P, 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'|
|DT||P, 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'|
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.
We thank all the third-party software providers used by this server: