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.

M3: an integrative framework for structure determination of molecular machines

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 […]

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 […]

Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes

This paper has recently been published in the Journal of Chemical Theory and Computation. Abstract Nucleotide-sequence-dependent interactions between proteins and DNA are responsible for a wide range of gene regulatory functions. Accurate and generalizable methods to evaluate the strength of protein–DNA binding have long been sought. While numerous computational approaches have […]

Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis

This paper is published in Data Science and Engineering, to appear in special issue “HPC-enabled Modelling for Big Data Problems in Life, Socio-Economical and Physical Sciences“. The Common Workflow Language is a core part of the Workflows component of BioExcel. Abstract Information integration and workflow technologies for data analysis have […]