Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design-Reference-Cited by-同舟云学术

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Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design

Published:2018-07 Issue:1 Volume:203 Page:54-61
ISSN:1047-8477
Container-title:Journal of Structural Biology
language:en
Short-container-title:Journal of Structural Biology

Author:

Ludwiczak Jan,Jarmula Adam^ORCID,Dunin-Horkawicz Stanislaw^ORCID

Funder

National Science Centre

Publisher

Elsevier BV

Subject

Structural Biology

Reference51 articles.

1. Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy;Alfarano;Protein Sci.,2012

2. The Rosetta all-atom energy function for macromolecular modeling and design;Alford;J. Chem. Theory Comput.,2017

3. Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface;Babor;Protein Sci.,2011

4. Accurate de novo design of hyperstable constrained peptides;Bhardwaj;Nature,2016

5. De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity;Boyken;Science,2016

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3. Predicting binding affinity changes from long‐distance mutations using molecular dynamics simulations and Rosetta;Proteins: Structure, Function, and Bioinformatics;2023-03-02

4. PDBench: evaluating computational methods for protein-sequence design;Bioinformatics;2023-01-01

5. Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation;Physical Chemistry Chemical Physics;2023

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