High-resolution protein complexes from integrating genomic information with molecular simulation

By Alexander Schug, Martin Weigt, José N. Onuchic, Terence Hwa, H. Szurmant. 2009

149 citations recorded by the source corpus.

Subfields: Genetics, Materials Chemistry, Molecular Biology

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Citations in the corpus

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1 (2015, neutral): “[44] Alexander Schug, Martin Weigt, José N Onuchic, Terence Hwa, and Hendrik Szurmant.”
Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, background): “Additional interesting potential applications include (2) a survey of the arrangements of trans-membrane segments in membrane proteins; (3) discovery of remote evolutionary homologies by comparison of 3D structures beyond the power of sequence profiles [78] (4) prediction of the assembly of domain s”
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information (2014, background): “As noted above, the accuracy of these models is reduced by the confounding of direct and indirect correlations ( Lapedes et al., 1999 ; Weigt et al., 2009 ); the application of global statistical models to coevolution-based contact prediction across interfaces has been limited to the case of the…”
Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners (2014, neutral): “Inferred contacts have been shown to be sufficient to guide the assembly of complexes between proteins of known (or homology modeled) monomer structure [24,25], and to predict the fold of single proteins [26–31], including highlights like large transmembrane proteins [28,31].”
Are Biological Systems Poised at Criticality? (2010, background): “[60] Alexander Schug, Martin Weigt, José N Onuchic, Terence Hwa, and Hendrik Szurmant, “High-resolution protein complexes from integrating genomic information with molecular simulation,” Proc Natl Acad Sci USA 106, 22124–9 (Dec 2009).”
Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes (2016, methodology): “3 ) obtained from DCA has been related to the theory of evolutionary sequence selection (Morcos et al. 2014) as well as mutational changes in protein stability (Lui and Tiana 2013; Morcos et al. 2014; Contini and Tiana 2015).”
How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins? (2018, methodology): “Methods like the direct coupling analysis (DCA) [8, 9], PsiCov [10] or Gremlin [11] allow for the prediction of residue-residue contacts using sequence information alone, and can be used to predict three-dimensional protein structures [12, 13] and to assemble protein complexes [14, 15, 16].”
From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction (2012, unknown): “The full potential of maximum-entropy modeling for accurate structural prediction was first recognized in [30] (quaternary structure prediction) and in [31] (tertiary structure prediction), and further applied by [32–38].”
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis (2012, methodology): “structures of protein complexes in silico when individual structures of the proteins are available (20, 21).”
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information (2014, methodology): “DCA has successfully been used to identify intradomain (23 – 27) and interdomain (16, 17, 23, 28) contacts in proteins, including the prediction of a transient HK/RR complex that is within crystallographic accuracy of the experimentally determined structure (6).”
3D Protein Structure Predicted from Sequence (2011, unknown): “Additional interesting potential applications include (2) a survey of the arrangements of trans-‐membrane segments in membrane proteins; (3) discovery of remote evolutionary homologies by comparison of 3D st”
Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis (2017, methodology): “studies using coevolutionary direct information (20).”
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis (2016, background): “contacts between bacterial signal transduction proteins, to help to assemble protein complexes (15, 16) and shed light on interaction specificity (17, 18).”
Limits and potential of combined folding and docking (2021, methodology): “In addition, co-evolution-based methods have also been used to predict the structure of complexes [9,17].”