News

Group Retreat 2019

Thirty members of Molecular Biophysics Stockholm, representing thirteen countries and a range of research areas, gathered for our annual spring retreat on 8 April 2019 at the Science for Life Laboratory in Solna, Sweden. Gabriella Fägerlind of Uppsala’s Implement Diversity AB led a workshop on inclusivity and psychological safety in the academic workplace, followed by small- and large-group exercises around goal-setting and group resource development, and an evening pizza party.

Publications

eBDIMS Server

Accepted manuscript, Bioinformatics 2019. Posted online ahead of print 19 February 2019

eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces

Laura Orellana, Johan Gustavsson, Cathrine Bergh, Ozge Yoluk, Erik Lindahl

Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial. Here, we present an online tool for transition pathway generation between two protein conformations using Elastic Network Driven Brownian Dynamics Importance Sampling, a coarse-grained simulation algorithm, which spontaneously predicts transition intermediates trapped experimentally. In addition to path-generation, the server provides an interactive 2D-motion landscape graphical representation of the transitions or any additional conformers to explore their structural relationships.

Read the full publication here.

Publications

How to create open access and reproducible molecular simulations

From January 10, 2019 release of PLOS Computational Biology (v. 15 pp. 1-4)

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist

All PLOS journals have an open data policy that, amongst other things, states that all data and related metadata underlying the findings reported in a submitted manuscript should be deposited in an appropriate public repository, or for smaller datasets, as supporting information. This should obviously apply to computational methods as well, but unfortunately this is not always applied in practice, although it is of greatest importance for the scientific quality of simulations and other modeling projects.

Molecular dynamics and other type of simulations have become a fundamental part of life sciences. The simulations are dependent on a number of parameters such as force fields, initial configurations, simulation protocols, and software. Researchers have different opinions about the types of software they prefer, and in general, we believe authors should be free to choose the tools that best fit their needs. However, as scientists, we also have a common obligation to critically test each other’s statements to find mistakes (including errors in the algorithms and bugs in the code), which can be exemplified by a heated debate over simulations of supercooled water that ended up being due to a subtle algorithmic issue, and we believe PLOS has a particularly strong responsibility to lead this development even if it might cause some short-term grief.

In particular, all published results should, in principle, be possible to reproduce independently by scientists in other labs using different tools. To ensure this, we propose a set of standards that any publication in PLOS Computational Biology, and hopefully, publications in other journals as well, should follow. We do believe that the sooner such policies are widely adapted, the more open and collaborative science will flourish.

These 10 simple rules should not be limited to molecular dynamics but also include Monte Carlo simulations, quantum mechanics calculations, molecular docking, and any other computational methods involving computations on biological molecules.

Read the full publication here.

Publications

e-Science in Scandinavia

From the December 2018 release of Informatik Spektrum (v. 41 pp. 398–404):

e-Science in Scandinavia: The Case of the Swedish e-Science Research Center

Olivia Eriksson, Erwin Laure, Erik Lindahl, Dan Henningson & Anders Ynnerman

The Swedish e-Science Research Centre (SeRC) is based on a collaboration between four Swedish universities: The KTH Royal Institute of Technology (KTH), Stockholm University (SU), Karolinska Institutet (KI) and Linköping University (LiU). SeRC’s mission statement is to develop state-of-the-art eScience tools and provide e-infrastructure support to existing and emerging e-Science research communities to help bring about scientific breakthroughs in Sweden. SeRC was founded in 2010 as the result of the Strategic Research Area (SRA) initiative launched by the Swedish Government Bill on Research Policy in 2008, where a total of 24 different strategic research areas were defined – one of which was e-Science. Initially SeRC was granted funding for 5 years. During those first 5 years, SeRC built up an organization for e-Science research, which has been highly successful. This was reflected in the excellent grades that SeRC received when the SRAs in Sweden were evaluated in 2015, and the fact that after this, SeRC received funding for at least 5 more years. This new phase of SeRC partly focuses on activities relating to emerging technologies (such as exascale systems and data-driven science) while also consolidating SeRC’s ongoing efforts in working towards a long-lasting e-Science environment in Sweden.

Read the full publication here.