Multipass membrane protein structure prediction using Rosetta

By Vladimir Yarov-Yarovoy, J. Schonbrun, David Baker. 2005

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Citations in the corpus

3D structures of membrane proteins from genomic sequencing (2012, neutral): “However, these calculations were limited in both protein size (%7 transmembrane helices) and accuracy, despite added information on helix-helix contact predictions from experimentally nonhomologous structures and a few known experimentally determined contacts (Barth et al., 2009; Yarov-Yarovoy et al”
Enhancing structure prediction and design of soluble and membrane proteins with explicit solvent-protein interactions (2017, methodology): “The same comparison was performed to assess the improved structural accuracy of RosettaMembrane with hybrid solvation compared to the starting template structure or the structures generated by the standard default mode of the homology modeling software Modeller (Eswar et al., 2008).”
Voltage-gated ion channels and gating modifier toxins. (2007, background): “2 atomic level gives a detailed view of the sliding helix movement of the S4 gating charges through a gating pore across the membrane upon depolarization and shows how the S4 S5 linker exerts a force on the pore-lining S6 segments to open the pore (– Yarov-Yarovoy et al., 2006 Toxicon .”
Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors (2013, methodology): “After each defined loop has been closed, resulting full sequence models were subjected to eight iterative cycles of side chain repacking and gradient minimization of w , y , and x angles using the Rosetta scoring function with an implicit membrane potential [32].”
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment (2011, unknown): “…2008; Chen et al., 2003; Davis and Baker, 2009; Eswar et al., 2006; Katritch et al., 2010; Lang et al., 2009; Morris et al., 2009; Vaidehi et al., 2002; Verdonk et al., 2003; Yarov-Yarovoy et al., 2006; Zhou andGilson, 2009) is complemented by great advances in computing resources and technologies.”
Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments (2008, methodology): “structure prediction algorithm Rosetta of Baker and co-workers [29–31], which also proved to be successful in accurately designing new folds [32].”
Recent advances in de novo protein design: Principles, methods, and applications (2021, methodology): “An early version of the Rosetta membrane scoring function (123) used statistics from 28 trans-membrane proteins to ﬁ t parameters and was validated by ab initio structure prediction of 12 multipass membrane proteins.”
An Integrated Framework Advancing Membrane Protein Modeling and Design (2015, methodology): “The RosettaMembrane ab initio protocol [23,26] was one of the first methods for ab initio structure prediction of membrane proteins.”
GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models (2018, methodology): “Additionally, due to three different scoring functions (Rosetta, Rosetta-MP, BCL::Score) it is possible to select accurate models for the required purposes: the structure of the binding site, the transmembrane domain or the overall shape of the receptor.”