Below is a list of related publications by the partners of the BioExcel consortium. We strive to publish as Open Access, or to provide green open access preprints where gold open access is not possible. Please let us know if you are unable to access any of our publications.

Targeting RNA structure in SMNS reverses spinal muscular atrophy molecular phenotypes.

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, […]

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2

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 […]

Defining distance restraints in HADDOCK

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 […]

Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations

Abstract Despite a large number of antiretroviral drugs targeting HIV-1 protease for inhibition, mutations in this protein during the course of patient treatment can render them inefficient. This emerging resistance inspired numerous computational studies of the HIV-1 protease aimed at predicting the effect of mutations on drug binding in terms […]