Literature DB >> 28960548

Integrative structure modeling with the Integrative Modeling Platform.

Benjamin Webb1, Shruthi Viswanath1, Massimiliano Bonomi2, Riccardo Pellarin3, Charles H Greenberg1, Daniel Saltzberg1, Andrej Sali1.   

Abstract

Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use.
© 2017 The Protein Society.

Keywords:  computational optimization; hybrid modeling; integrative modeling; structural biology

Mesh:

Year:  2017        PMID: 28960548      PMCID: PMC5734277          DOI: 10.1002/pro.3311

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  90 in total

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6.  Population-based 3D genome structure analysis reveals driving forces in spatial genome organization.

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7.  PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.

Authors:  Stephen K Burley; Genji Kurisu; John L Markley; Haruki Nakamura; Sameer Velankar; Helen M Berman; Andrej Sali; Torsten Schwede; Jill Trewhella
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Authors:  Dina Schneidman-Duhovny; Michal Hammel; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2010-05-27       Impact factor: 16.971

Review 9.  The structural dynamics of macromolecular processes.

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  36 in total

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3.  CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation.

Authors:  Axel F Brilot; Andrew S Lyon; Alex Zelter; Shruthi Viswanath; Alison Maxwell; Michael J MacCoss; Eric G Muller; Andrej Sali; Trisha N Davis; David A Agard
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7.  Glutamine Side Chain 13C═18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly.

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8.  Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure.

Authors:  Daniel J Saltzberg; Shruthi Viswanath; Ignacia Echeverria; Ilan E Chemmama; Ben Webb; Andrej Sali
Journal:  Protein Sci       Date:  2020-12-03       Impact factor: 6.725

9.  In-cell architecture of the nuclear pore and snapshots of its turnover.

Authors:  Matteo Allegretti; Christian E Zimmerli; Vasileios Rantos; Florian Wilfling; Paolo Ronchi; Herman K H Fung; Chia-Wei Lee; Wim Hagen; Beata Turoňová; Kai Karius; Mandy Börmel; Xiaojie Zhang; Christoph W Müller; Yannick Schwab; Julia Mahamid; Boris Pfander; Jan Kosinski; Martin Beck
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Review 10.  FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.

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