This group is for users who have an interest in the structural prediction of biomolecular interactions combining experimental data from various sources with powerful algorithms to generate high-resolution 3D models of the macromolecular complexes. The time has come to ‘combine and conquer’.
Every month, a newsletter will be sent to the subscribers with a gathering of the latest news, major-impact publications, interviews of creator/developer of software that shape the field, etc. You can find below the last posts featured in our past newsletters:
Our first newsletter is released! Subscribe to the Integrative Modelling interest group if you want to receive every month the latest news over Integrative Modelling in your mailbox. And find below the newsletter you might have missed:
- May 23, 2017 : Integrative Modelling IG newsletter #2
- February 2, 2017 : Integrative Modelling IG newsletter #1
- October 10, 2016 : Integrative Modelling webinar series - PRODIGY web server (12/10/2016)
- 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 (Rockefeller University, New […] Read More
- Mathieu Montes is a professor at Conservatoire National des Arts et des Métiers (CNAM) in Paris, FRANCE. After a PhD (2007) in Université Paris Descartes, where he worked on the development and applications of drug-design and in silico screening techniques, Mathieu became assistant professor in molecular modelling and the head of a drug-design group at the CNAM […] Read More
Paper: Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assembliesAbstract 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 […] Read More
- 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 […] Read More
- Abstract Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, on October 6 and 7, 2014. At the […] Read More
Tips & Tricks
- Introduction GROMACS is a well-known and broadly used suite for molecular dynamics simulations. It is a free, open-source software that supports several force-fields (GROMOS, AMBER, CHARM, etc …) and is one of the flagship software within BioExcel. PyMol is a popular 3D molecular visualization system, maintained and distributed by Schrödinger on an open-source foundation. It […] Read More
- Many tasks we are performing in Integrative Modelling involve 3D structures of molecules. Visualising them, modifying them to fit a particular program requirements or just parsing them to analyse them can sometimes be time-consuming. We are presenting here two approaches to quickly and easily manipulate PDB files. Shell scripting (based on PDB-tools suite) Several short and efficient python […] Read More
Discuss Integrative Modelling
Discussions in this interest group are underway in the following categories at ask.bioexcel.eu:
This category is for all discussions related Integrative Structural Biology and Modelling, offering a forum to discuss various approaches and software. Please also register at http://bioexcel.eu/interest-groups to receive our newsletter.
The HADDOCK category is meant for discussing any topic related to the use of the HADDOCK software, either as a local installation or via the HADDOCK web portal. For details about HADDOCK please refer to http://www.bonvinlab.org/software/haddock2.2.
BioExcel Webinars related to Integrative Modelling
- Webinar #1: Integrative modelling of biomolecular complexes with HADDOCK – 29/04/2016 – Video in the link
- Webinar #7: PRODIGY, a web server to predict binding affinities in protein-protein complexes – 12/10/2016 – Video in the link
- Webinar #10: Robust solutions for cryoEM fitting and visualisation of interaction space – 15/02/2017 – Video in the link