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 […]
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 […]
Do you need to write correct software for your science? Will your software need to change over time? Do you need to make your software faster, or more scalable? How will your users learn how to use your software? How will you convince people to invest in your software? What […]
We are pleased to announce the publication of this paper in the journal Scientific Reports. Abstract We present SpotOn, a web server to identify and classify interfacial residues as Hot-Spots (HS) and Null-Spots (NS). SpotON implements a robust algorithm with a demonstrated accuracy of 0.95 and sensitivity of 0.98 on an […]
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 […]
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 […]