Macromolecular modeling and design in Rosetta: recent methods and frameworks
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 …
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
…, DE Kim, S Lyskov, M Berrondo, S Mentzer… - Methods in …, 2011 - Elsevier
… to the backbone, s, where the assignment to residue i, s i ∈ S i . The rotamer-vector search
space is the Cartesian product of the individual rotamer spaces: S = ∏ i S i . This problem is …
space is the Cartesian product of the individual rotamer spaces: S = ∏ i S i . This problem is …
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
S Chaudhury, S Lyskov, JJ Gray - Bioinformatics, 2010 - academic.oup.com
PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling
package that allows users to write custom structure prediction and design algorithms using …
package that allows users to write custom structure prediction and design algorithms using …
The RosettaDock server for local protein–protein docking
S Lyskov, JJ Gray - Nucleic acids research, 2008 - academic.oup.com
The RosettaDock server ( http://rosettadock.graylab.jhu.edu ) identifies low-energy conformations
of a protein–protein interaction near a given starting configuration by optimizing rigid-…
of a protein–protein interaction near a given starting configuration by optimizing rigid-…
[HTML][HTML] Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)
The Rosetta molecular modeling software package provides experimentally tested and
rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, …
rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, …
Scientific benchmarks for guiding macromolecular energy function improvement
Accurate energy functions are critical to macromolecular modeling and design. We describe
new tools for identifying inaccuracies in energy functions and guiding their improvement, …
new tools for identifying inaccuracies in energy functions and guiding their improvement, …
Modeling and docking of antibody structures with Rosetta
BD Weitzner, JR Jeliazkov, S Lyskov, N Marze… - Nature protocols, 2017 - nature.com
We describe Rosetta-based computational protocols for predicting the 3D structure of an
antibody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (…
antibody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (…
[HTML][HTML] Better together: Elements of successful scientific software development in a distributed collaborative community
…, AM Watkins, VK Mulligan, S Lyskov… - PLoS computational …, 2020 - journals.plos.org
… We further have a MediaWiki[37] since the early 2000’s communicating announcements
for conferences and teleconferences. Most of the documentation has moved to a Gollum wiki[38]…
for conferences and teleconferences. Most of the documentation has moved to a Gollum wiki[38]…
[HTML][HTML] Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability
Reengineering protein surfaces to exhibit high net charge, referred to as “supercharging”,
can improve reversibility of unfolding by preventing aggregation of partially unfolded states. …
can improve reversibility of unfolding by preventing aggregation of partially unfolded states. …
Peptiderive server: derive peptide inhibitors from protein–protein interactions
Y Sedan, O Marcu, S Lyskov… - Nucleic acids …, 2016 - academic.oup.com
… to experimental peptide arrays, in which an array is prepared that contains overlapping
peptides derived from one protein, to which the protein partner is added to identify the region(s) …
peptides derived from one protein, to which the protein partner is added to identify the region(s) …