LMP1 binding peptide and the TNFR-associated factor 2

In this example of protein-peptide docking, we select in step 2 a couple of residue restraints in the receptor partner (TNRF2) (A.411 and A.466). 1czy In step 3, we enable flexibility on both receptor and ligand partners.

DnaA domainIV complexed with DnaAbox DNA

In this example of protein-DNA docking, we select in step 2 a single residue restraint to drive the docking in the receptor partner (DnaA domainIV) (A.443). 1j1v In step 3, we enable flexibility on both receptor and ligand partners.

Inhibition of the Sonic Hedgehog metalloprotease by the anti-Shh 5E1 antibody

In this example of antibody-antigen docking, we show the automatic antibody mode to drive the docking. We select as receptor partner the anti-Shh 5E1 antibody molecule and the Sonic Hedgehog metalloprease as the ligand partner. After selecting the correct numbering of the input antibody PDB file (Chothia), in step 3 residue restraints are displayed in pink color, corresponding with the CDR loops. 3mxw Flexibility for both partners is activated in step 3.

Integrative modeling of Claudin-19 in complex with the C-CPE enterotoxin

In this integrative modeling example, we make use of a simulated coarse-grained bi-lipidic membrane as explained in the official LightDock tutorial and published in Integrative Modeling of Membrane-associated Protein Assemblies (Roel-Touris J, Jiménez-García B. and Bonvin AMJJ.) Nat Commun 11, 6210 (2020). 3x29 Once the provided receptor PDB file is uploaded to the server, we select the molecule type as membrane. No further restraints are selected in this example.