Collaborative partnership with Vrije Universiteit Amsterdam

Vrije Universiteit Amsterdam is now a collaborative partner of BioExcel. Within the Division of Molecular and Computational Toxicology at Vrije Universiteit Amsterdam (VUA), the Biomolecular Simulation and Modeling team develops, implements and applies advanced in silico models to study and predict protein-ligand binding from (HPC) simulation. In the context of the IMI-JU eTOX project and […]

Webinar: “MDStudio, microservice based molecular dynamics workflows” (2017-10-11)

BioExcel’s webinar series continue with an introduction of the workflow tool, MDStudio. The webinar is part of the collaborative work plan between BioExcel and Vrije Universiteit Amsterdam. Abstract Molecular Dynamics (MD) is becoming an essential method in the research toolkit of academic and applied science. Common practice is to combine MD with other in silico modelling, […]

BioExcel establishes a partnership with MolSSI

We are happy to announce our new official partnership with the Molecular Sciences Software Institute (MolSSI). MolSSI serves as a nexus for science, education, and cooperation serving the worldwide community of computational molecular scientists. The Institute supports advances in software infrastructure, education, standards, and best-practices that are needed to enable the molecular science community to […]

GROMACS Release 2016.4

Hi GROMACS users, The official release of GROMACS 2016.4 is available! This release fixes several issues found since 2016.3, including disabling the broken support for automatic PME tuning in mdrun for group-scheme simulations, and various other fixes. It also implements production-ready support for CUDA 9 + Volta generation GPUs, along with other portability enhancements. It incorporates all the fixes found in the […]

ChimeraX, a new version of Chimera available on SBgrid

Introduction UCSF Chimera is one of the most popular molecular viewer. It is currently developed by the Resource for Biocomputing, Visualization, and Informatics at University of California, San Francisco. Among its many features, Chimera is probably the best software for the interactive visualisation and analysis density maps. It allows for a fine-tuning of the density maps and […]

Lights on… Matteo Dal Peraro, creator of power

Matteo Dal Peraro graduated in Physics at the University of Padua in 2000. He obtained his Ph.D. in Biophysics at the International School for Advanced Studies (SISSA, Trieste) in 2004. He then received postdoctoral training at the University of Pennsylvania (Philadelphia) under the guidance of Prof. M. L. Klein. He was nominated Tenure Track Assistant Professor […]

Review: Integrative modelling of cellular assemblies

Abstract A wide variety of experimental techniques can be used for understanding the precise molecular mechanisms underlying the activities of cellular assemblies. The inherent limitations of a single experimental technique often requires integration of data from complementary approaches to gain sufficient insights into the assembly structure and function. Here, we review popular computational approaches for […]

Paper: Capturing protein communities by structural proteomics in a thermophilic eukaryote

Abstract The arrangement of proteins into complexes is a key organizational principle for many cellular functions. Although the topology of many complexes has been systematically analyzed in isolation, their molecular sociology in situ remains elusive. Here, we show that crude cellular extracts of a eukaryotic thermophile, Chaetomium thermophilum, retain basic principles of cellular organization. Using a structural proteomics approach, […]

Try looking in the monthly archives. September 2017