Macromolecular modeling and design in Rosetta: recent methods and frameworks

…, S Lindert, T Linsky, N London, JH Lubin, S Lyskov… - 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 …

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 …

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 …

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-…

[HTML][HTML] Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)

S Lyskov, FC Chou, SO Conchuir, BS Der, K Drew… - PloS one, 2013 - journals.plos.org
The Rosetta molecular modeling software package provides experimentally tested and
rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, …

Scientific benchmarks for guiding macromolecular energy function improvement

…, J Thompson, IW Davis, RA Pache, S Lyskov… - Methods in …, 2013 - Elsevier
Accurate energy functions are critical to macromolecular modeling and design. We describe
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 (…

[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]…

[HTML][HTML] Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability

BS Der, C Kluwe, AE Miklos, R Jacak, S Lyskov… - PloS one, 2013 - journals.plos.org
Reengineering protein surfaces to exhibit high net charge, referred to as “supercharging”,
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) …