Literature DB >> 30049874

Biophysical experiments and biomolecular simulations: A perfect match?

Sandro Bottaro1, Kresten Lindorff-Larsen2.   

Abstract

A fundamental challenge in biological research is achieving an atomic-level description and mechanistic understanding of the function of biomolecules. Techniques for biomolecular simulations have undergone substantial developments, and their accuracy and scope have expanded considerably. Progress has been made through an increasingly tight integration of experiments and simulations, with experiments being used to refine simulations and simulations used to interpret experiments. Here we review the underpinnings of this progress, including methods for more efficient conformational sampling, accuracy of the physical models used, and theoretical approaches to integrate experiments and simulations. These developments are enabling detailed studies of complex biomolecular assemblies.
Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Mesh:

Year:  2018        PMID: 30049874     DOI: 10.1126/science.aat4010

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  36 in total

Review 1.  The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins.

Authors:  Rajeswari Appadurai; Vladimir N Uversky; Anand Srivastava
Journal:  J Membr Biol       Date:  2019-05-28       Impact factor: 1.843

2.  Comparing mutagenesis and simulations as tools for identifying functionally important sequence changes for protein thermal adaptation.

Authors:  Ming-Ling Liao; George N Somero; Yun-Wei Dong
Journal:  Proc Natl Acad Sci U S A       Date:  2018-12-24       Impact factor: 11.205

3.  Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation.

Authors:  Utsab R Shrestha; Puneet Juneja; Qiu Zhang; Viswanathan Gurumoorthy; Jose M Borreguero; Volker Urban; Xiaolin Cheng; Sai Venkatesh Pingali; Jeremy C Smith; Hugh M O'Neill; Loukas Petridis
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-23       Impact factor: 11.205

4.  Assessing Structural Preferences of Unstructured Protein Regions by NMR.

Authors:  Azzurra Carlon; Lucia Gigli; Enrico Ravera; Giacomo Parigi; Angela M Gronenborn; Claudio Luchinat
Journal:  Biophys J       Date:  2019-10-14       Impact factor: 4.033

5.  Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations.

Authors:  Yen-Lin Chen; Weiwei He; Serdal Kirmizialtin; Lois Pollack
Journal:  Cell Rep Phys Sci       Date:  2022-07-11

6.  Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure.

Authors:  Ryan J Emenecker; Daniel Griffith; Alex S Holehouse
Journal:  Biophys J       Date:  2021-09-02       Impact factor: 3.699

7.  Best Practices for Foundations in Molecular Simulations [Article v1.0].

Authors:  Efrem Braun; Justin Gilmer; Heather B Mayes; David L Mobley; Jacob I Monroe; Samarjeet Prasad; Daniel M Zuckerman
Journal:  Living J Comput Mol Sci       Date:  2018-11-29

8.  Martini 3: a general purpose force field for coarse-grained molecular dynamics.

Authors:  Paulo C T Souza; Riccardo Alessandri; Jonathan Barnoud; Sebastian Thallmair; Ignacio Faustino; Fabian Grünewald; Ilias Patmanidis; Haleh Abdizadeh; Bart M H Bruininks; Tsjerk A Wassenaar; Peter C Kroon; Josef Melcr; Vincent Nieto; Valentina Corradi; Hanif M Khan; Jan Domański; Matti Javanainen; Hector Martinez-Seara; Nathalie Reuter; Robert B Best; Ilpo Vattulainen; Luca Monticelli; Xavier Periole; D Peter Tieleman; Alex H de Vries; Siewert J Marrink
Journal:  Nat Methods       Date:  2021-03-29       Impact factor: 28.547

Review 9.  Physics-based computational and theoretical approaches to intrinsically disordered proteins.

Authors:  Joan-Emma Shea; Robert B Best; Jeetain Mittal
Journal:  Curr Opin Struct Biol       Date:  2021-02-02       Impact factor: 6.809

10.  Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems.

Authors:  Ilya Kuprov; Laura C Morris; John N Glushka; James H Prestegard
Journal:  J Magn Reson       Date:  2020-12-13       Impact factor: 2.229

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