Publications

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.


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 […]


Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

The paper Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data was published in PLoS Biology in June 2017. The authors, which includes experts from well-recognized data providers like Uniprot and EMBL-EBI, describe the lessons learnt when […]