Webinar: “Introduction to the Common Workflow Language (CWL) project” (2017-06-21)

Discuss this webinar View slides View webinar Workflows Interest Group BioExcel’s webinar series continues with Michael Crusoe, CWL Project co-founder & Community Engineer, who will introduce the Common Workflow Language (CWL) project. In July 2016 the CWL team released standards that enable the portable, interoperable, and executable description of command line data analysis tools and workflow made from those tools. […]

BioExcel Introductory Video

We completed the production of our new introductory video “Presenting BioExcel: A central hub for biomolecular modelling and simulations “! Learn about our center in just a few minutes! Kudos to Apostolos Vasileiadis from Third Pända Film for the great production! Check out his work Facebook, Twitter, Instagram and Vimeo.

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update

This paper was published in Nucleic Acids Research in 2017. Abstract We present here a full update of the PMut predictor, active since 2005 and with a large acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine has been renewed, and converted into a fully featured standalone training and prediction engine that […]

The pmx Webserver: a Powerful Tool for Free Energy Calculations

BioExcel supports the development of pmx, a tool for researchers utilising free energy calculations. Free energy calculations are extremely common in life sciences research. In molecular dynamics simulations, such as investigating how mutations affect protein function, these calculations provide insight into stability and affinity changes. One important branch of free energy calculations involve alchemical transformations […]

Environment meets genetics: New lessons for Parkinson’s disease

FZ Jülich, a BioExcel partner, is using CPMD, a leading QM/MM software package, to understand more about how Parkinson’s disease develops. Parkinson’s disease (PD) is a devastating disorder, affecting a growing number of people worldwide, due to the overall aging of the human population. The disease is known for its typical motor problems (tremor, muscular […]

Paper: Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

Abstract Predicting the structure of large molecular assemblies remains a challenging task in structural biology when using integrative modeling approaches. One of the main issues stems from the treatment of heterogeneous experimental data used to predict the architecture of native complexes. We propose a new method, applied here for the first time to a set […]

Paper: Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex

Abstract The membrane ring that equatorially circumscribes the nuclear pore complex (NPC) in the perinuclear lumen of the nuclear envelope is composed largely of Pom152 in yeast and its ortholog Nup210 (or Gp210) in vertebrates. Here, we have used a combination of negative-stain electron microscopy, nuclear magnetic resonance, and small-angle X-ray scattering methods to determine […]

HADDOCK shows how bacteria steal iron from the plants they infect

Researchers using the HADDOCK modelling software, a key part of the BioExcel community, have discovered how bacteria steal iron from plants, helping the bacteria cause infection. Iron is an essential element for life. Mammals, for example, use it to carry oxygen in red blood cells, plants need it to transport electrons. Bacteria are not an […]

GROMACS researcher position in Stockholm

Do you want to join BioExcel as a researcher working with GROMACS? We have an open position right now. Deadline for application – June 16th. As part of this center, we seek a researcher who will work with development of algorithms, programs and computational techniques focused on molecular dynamics, in particular on GROMACS. The duties […]

pmx Webserver: A User Friendly Interface for Alchemistry

This paper describes the pmx webserver, part of the BioExcel community. The paper was published in February 2017 in the Journal of Chemical Information and Modelling. Abstract With the increase of available computational power and improvements in simulation algorithms, alchemical molecular dynamics based free energy calculations have developed into routine usage. To further facilitate the […]

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