Macromolecular modeling and design in Rosetta: recent methods and frameworks
JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …
in laboratories worldwide. During two decades of development by a community of …
On the binding affinity of macromolecular interactions: daring to ask why proteins interact
PL Kastritis, AMJJ Bonvin - Journal of The Royal Society …, 2013 - royalsocietypublishing.org
Interactions between proteins are orchestrated in a precise and time-dependent manner,
underlying cellular function. The binding affinity, defined as the strength of these …
underlying cellular function. The binding affinity, defined as the strength of these …
Principles and overview of sampling methods for modeling macromolecular structure and dynamics
T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …
how macromolecules carry out their functions in the cell. Significant advances have been …
Protocols for molecular modeling with Rosetta3 and RosettaScripts
Previously, we published an article providing an overview of the Rosetta suite of
biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, KW …
biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, KW …
Protein dynamics and function from solution state NMR spectroscopy
M Kovermann, P Rogne, M Wolf-Watz - Quarterly reviews of …, 2016 - cambridge.org
It is well-established that dynamics are central to protein function; their importance is
implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of …
implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of …
Integrative structural biology
Biological assemblies and machines often elude structural characterization, hampering our
understanding of how they function, how they evolved, and how they can be modulated. A …
understanding of how they function, how they evolved, and how they can be modulated. A …
Modeling symmetric macromolecular structures in Rosetta3
F DiMaio, A Leaver-Fay, P Bradley, D Baker, I André - PloS one, 2011 - journals.plos.org
Symmetric protein assemblies play important roles in many biochemical processes.
However, the large size of such systems is challenging for traditional structure modeling …
However, the large size of such systems is challenging for traditional structure modeling …
NMR approaches for structural analysis of multidomain proteins and complexes in solution
NMR spectroscopy is a key method for studying the structure and dynamics of (large)
multidomain proteins and complexes in solution. It plays a unique role in integrated …
multidomain proteins and complexes in solution. It plays a unique role in integrated …
Recent advances in NMR protein structure prediction with ROSETTA
J Koehler Leman, G Künze - International Journal of Molecular Sciences, 2023 - mdpi.com
Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for studying the
structure and dynamics of proteins in their native state. For high-resolution NMR structure …
structure and dynamics of proteins in their native state. For high-resolution NMR structure …
[HTML][HTML] Hybrid methods for combined experimental and computational determination of protein structure
JT Seffernick, S Lindert - The Journal of chemical physics, 2020 - pubs.aip.org
Knowledge of protein structure is paramount to the understanding of biological function,
develo** new therapeutics, and making detailed mechanistic hypotheses. Therefore …
develo** new therapeutics, and making detailed mechanistic hypotheses. Therefore …