Abstract We report the performance of HADDOCK in the 2018 iteration of the Grand Challenge organised by the D3R consortium. Building on the findings of our participation in last year’s challenge, we significantly improved our pose prediction protocol which resulted in a mean RMSD for the top scoring pose of […]
This paper was published in Nature Methods in August 2017. Abstract We present a broadly applicable, user-friendly protocol that incorporates sparse and hybrid experimental data to calculate quasi-atomic-resolution structures of molecular machines. The protocol uses the HADDOCK framework, accounts for extensive structural rearrangements both at the domain and atomic levels […]
This paper was published in Nature Communications in May 2018. Abstract Modification of SMN2 exon 7 (E7) splicing is a validated therapeutic strategy against spinal muscular atrophy (SMA). However, a target-based approach to identify small-molecule E7 splicing modifiers has not been attempted, which could reveal novel therapies with improved mechanistic insight. Here, […]
This paper was published in the Biophysical Journal in May 2018. Abstract Human mitochondrial transcription factor A (TFAM) distorts DNA into a U-turn, as shown by crystallographic studies. The relevance of this U-turn is associated with transcription initiation at the mitochondrial light strand promoter (LSP). However, it has not been […]
Abstract We present the performance of HADDOCK, our information-driven docking software, in the second edition of the D3R Grand Challenge. In this blind experiment, participants were requested to predict the structures and binding affinities of complexes between the Farnesoid X nuclear receptor and 102 different ligands. The models obtained in […]
Abstract In a recent issue of Nature Protocols, Orbán-Németh et al.1 present a protocol to predict structural models of proteins and their complexes from mass spectrometry (MS) cross-linking data. We read the protocol with interest, as it uses third-party software including the HADDOCK web portal2 that we developed and maintain. While […]