Literature DB >> 23267861

Advances in integrative modeling of biomolecular complexes.

Ezgi Karaca1, Alexandre M J J Bonvin.   

Abstract

High-resolution structural information is needed in order to unveil the underlying mechanistic of biomolecular function. Due to the technical limitations or the nature of the underlying complexes, acquiring atomic resolution information is difficult for many challenging systems, while, often, low-resolution biochemical or biophysical data can still be obtained. To make best use of all the available information and shed light on these challenging systems, integrative computational tools are required that can judiciously combine and accurately translate sparse experimental data into structural information. In this review we discuss the current state of integrative approaches, the challenges they are confronting and the advances made regarding those challenges. Recent developments are underpinned by noteworthy application examples taken from the literature. Within this context, we also position our data-driven docking approach, HADDOCK that can integrate a variety of information sources to drive the modeling of biomolecular complexes. Only a synergistic combination of experiment and modeling will allow us to tackle the challenges of adding the structural dimension to interactomes, shed "atomic" light onto molecular processes and understand the underlying mechanistic of biomolecular function. The current state of integrative approaches indicates that they are poised to take those challenges.
Copyright © 2012 Elsevier Inc. All rights reserved.

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Year:  2012        PMID: 23267861     DOI: 10.1016/j.ymeth.2012.12.004

Source DB:  PubMed          Journal:  Methods        ISSN: 1046-2023            Impact factor:   3.608


  24 in total

1.  M3: an integrative framework for structure determination of molecular machines.

Authors:  Ezgi Karaca; João P G L M Rodrigues; Andrea Graziadei; Alexandre M J J Bonvin; Teresa Carlomagno
Journal:  Nat Methods       Date:  2017-08-14       Impact factor: 28.547

2.  Sequence co-evolution gives 3D contacts and structures of protein complexes.

Authors:  Thomas A Hopf; Charlotta P I Schärfe; João P G L M Rodrigues; Anna G Green; Oliver Kohlbacher; Chris Sander; Alexandre M J J Bonvin; Debora S Marks
Journal:  Elife       Date:  2014-09-25       Impact factor: 8.140

Review 3.  Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology.

Authors:  Clinton Yu; Lan Huang
Journal:  Anal Chem       Date:  2017-11-21       Impact factor: 6.986

4.  Identification of a ubiquitin-binding interface using Rosetta and DEER.

Authors:  Maxx H Tessmer; David M Anderson; Adam M Pickrum; Molly O Riegert; Rocco Moretti; Jens Meiler; Jimmy B Feix; Dara W Frank
Journal:  Proc Natl Acad Sci U S A       Date:  2018-01-02       Impact factor: 11.205

Review 5.  Membrane association of the PTEN tumor suppressor: neutron scattering and MD simulations reveal the structure of protein-membrane complexes.

Authors:  Hirsh Nanda; Frank Heinrich; Mathias Lösche
Journal:  Methods       Date:  2014-10-27       Impact factor: 3.608

6.  A decadentate Gd(III)-coordinating paramagnetic cosolvent for protein relaxation enhancement measurement.

Authors:  Xin-Hua Gu; Zhou Gong; Da-Chuan Guo; Wei-Ping Zhang; Chun Tang
Journal:  J Biomol NMR       Date:  2014-02-09       Impact factor: 2.835

Review 7.  Structural bioinformatics of the interactome.

Authors:  Donald Petrey; Barry Honig
Journal:  Annu Rev Biophys       Date:  2014       Impact factor: 12.981

8.  Mass spec studio for integrative structural biology.

Authors:  Martial Rey; Vladimir Sarpe; Kyle M Burns; Joshua Buse; Charles A H Baker; Marc van Dijk; Linda Wordeman; Alexandre M J J Bonvin; David C Schriemer
Journal:  Structure       Date:  2014-09-18       Impact factor: 5.006

9.  Assessment of the CASP14 assembly predictions.

Authors:  Burcu Ozden; Andriy Kryshtafovych; Ezgi Karaca
Journal:  Proteins       Date:  2021-08-31

Review 10.  Sparse labeling of proteins: structural characterization from long range constraints.

Authors:  James H Prestegard; David A Agard; Kelley W Moremen; Laura A Lavery; Laura C Morris; Kari Pederson
Journal:  J Magn Reson       Date:  2014-04       Impact factor: 2.229

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