HADDOCK2.4 antibody-antigen docking tutorial: This tutorial demonstrates the use of HADDOCK2.4 for predicting the structure of an antibody-antigen complex using information about the hypervariable loops of the antibody and either the entire surface of the antigen or a loose definition of the epitope. This tutorial does not require any Linux expertise and only makes use of our web servers and...
HADDOCK3 antibody-antigen docking: This tutorial demonstrates the use of HADDOCK3 for predicting the structure of an antibody-antigen complex using information about the hypervariable loops of the antibody and either the entire surface of the antigen or a loose definition of the epitope. It illustrate the modularity of HADDOCK3 by introducing a new workflow not possible under the current...
The Distance Geometry Problem (DGP) asks whether a simple weighted undirected graph G=(V,E,d) can be realized in the K-dimensional Euclidean space so that the distance constraints implied by the weights on the graph edges are satisfied. This problem was proven to be NP-hard in the context of graph embeddability, and has several applications. In this talk, we will focus on various currently...
Protein-protein and protein-ligand interactions are central in biological mechanisms. These interactions can be classified into thermodynamics and mechanistic pathways. Estimating accurate and reliable interaction energetics along the thermodynamic pathway is one of the ongoing challenges in computational biophysics. Umbrella sampling simulation-based potential of mean force calculations is...
It has been estimated based on the graph theory that there are at least 1060 organic molecules that are relevant for small-molecule drug discovery. Using machine learning to estimate the binding free energies for screening of large chemical libraries to search for the tightly binding inhibitors would take a considerable amount of computational resources, yet it is not possible to explore the...
