Dear reader reader,

Here is the second newsletter in our Integrative Modelling series. If you missed the first one, you can luckily still find it here.

This month, we scale up! This was the least we could do to apologize for the delay consecutive to some technical issues on the web server. Everything is now back to normal so here is the program: 

Two freshly baked publications instead of one, the interview of Marc Marti-Renom who created TADbit, a framework to model the 3D structure and dynamics of the genome based on 3C data and a recent PyMOL plugin to perform MD simulations directly from your molecular viewer. 

We hope to trigger some discussions on the interest group and really encourage you to contribute to the upcoming issues of our newsletter by suggesting events/articles on the IG-IM forum.

As usual, a digest of all those posts can be found on the main page of our community.


Lights on... Marc Marti-Renom - creator of TADbit

Marc Martí-Renom is a professor at the Catalan Institution for Research and Advanced Studies (ICREA) in Barcelona (Spain). After a Ph.D. in Biophysics from the Autonomous University of Barcelona (UAB) where he worked on protein folding under the supervision of Professors B. Oliva, F.X. Avilés and M. Karplus (Nobel Laureate in 2013), Marc joined the Sali Lab for a postdoctoral fellowship on protein structure modelling. Since October 2013, he is full time research Professor at ICREA and leads the CNAG and the CRG, both in Barcelona. In the past few years, they developed TADbit, a python library that extend the modelling capacities of IMP to study the structure of genome or genomic domains based on high-throughput chromatin conformation capture (3C) data. Read more



G. Tamò et al. (2017)
Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies
Scientific Reports, 7(1), Article 235.
SUMMARY: 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 of symmetrical complexes, based on evolutionary computation...Read more

P. Upla et al. (2017)
Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex
Structure, Volume 25, Issue 3, 434-445.
SUMMARY: 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 an integrative structure of the ∼120 kDa luminal domain of Pom152. Our structural analysis reveals... Read more


Tips & Tricks

Today, we will introduce a new PyMol plugin, Dynamics, that aims to bring GROMACS at the core of your favorite molecular viewer!
Do not hesitate to share your own tips & tricks!