Integrative Modelling IG


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:

News

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:

Interviews

  • Lights on… Matteo Dal Peraro, creator of power

    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 […] Read More
  • Lights on… Marc Marti-Renom, creator of TADbit

    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 (Rockefeller University, New […] Read More
  • Lights on… Mathieu Montes, co-creator of UDock

    Lights on… Mathieu Montes, co-creator of UDock

    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

Publications

  • Review: Integrative modelling of cellular assemblies

    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 […] Read More
  • Paper: Capturing protein communities by structural proteomics in a thermophilic eukaryote

    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, […] Read More
  • Paper: Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

    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 […] Read More
  • Paper: Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex

    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 […] Read More
  • Paper: Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

    Paper: Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

    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

  • ChimeraX, a new version of Chimera available on SBgrid

    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 […] Read More
  • Run GROMACS within PyMol with Dynamics

    Run GROMACS within PyMol with Dynamics

    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
  • Parse and manipulate PDB files with shell and PyMol

    Parse and manipulate PDB files with shell and PyMol

    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:

Integrative Modelling IG

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.

HADDOCK

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