Proteins: Structure, Function and Bioinformatics

Journal: Proteins: Structure, Function and Bioinformatics

Abbreviation

Proteins

Publisher

Wiley-Blackwell

ISSN

0887-3585
1097-0134

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Publications 1 - 10 of 29

Protein under pressure
Trzesniak, Daniel; Lins, Roberto D.; van Gunsteren, Wilfred F. (2006)
Proteins: Structure, Function and Bioinformatics
What stabilizes the 3(14)-helix in β(3)-peptides?
Keller, Bettina; Gattin, Zrinka; van Gunsteren, Wilfred F. (2010)
Proteins: Structure, Function and Bioinformatics
Biological and functional relevance of CASP predictions
Liu, Tianyun; Ish‐Shalom, Shirbi; Torng, Wen; et al. (2018)
Proteins: Structure, Function and Bioinformatics
Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo‐sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo‐sites), and Ten sites containing important motifs, loops, or key residues with important disease‐associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best‐ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand‐binding sites, most prediction methods have higher performance on apo‐sites than holo‐sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein‐protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein‐protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template.
Protein-based virtual screening of chemical databases
Bissantz, Caterina; Bernard, Philippe; Hibert, Marcel; et al. (2003)
Proteins: Structure, Function and Bioinformatics
Relative tolerance of mesostable and thermostable protein scaffolds to extensive mutation
Besenmatter, Werner; Kast, Peter; Hilvert, Donald (2007)
Proteins: Structure, Function and Bioinformatics
NMR structure of the conserved hypothetical protein TM0979 from Thermotoga maritima
Peti, Wolfgang; Herrmann, Torsten; Zagnitko, Olga; et al. (2005)
Proteins: Structure, Function and Bioinformatics
Conformational transitions driven by pyridoxal-5 '-phosphate uptake in the psychrophilic Serine hydroxymethyltransferase from Psychromonas ingrahamii
Angelaccio, Sebastiana; Dworkowski, Florian; Di Bello, Angela; et al. (2014)
Proteins: Structure, Function and Bioinformatics
Molecular dynamics simulations of peptides containing an unnatural amino acid
Yu, Haibo; Daura, Xavier; van Gunsteren, Wilfred F. (2004)
Proteins: Structure, Function and Bioinformatics
NMR structure determination of the conserved hypothetical protein TM1816 from Thermotoga maritima
Columbus, Linda; Peti, Wolfgang; Etezady-Esfarjani, Touraj; et al. (2005)
Proteins: Structure, Function and Bioinformatics
Dual-affinity avidin molecules
Hytönen, Vesa P.; Nordlund, Henri R.; Hörhä, Jarno; et al. (2005)
Proteins: Structure, Function and Bioinformatics

Publications 1 - 10 of 29

Journal: Proteins: Structure, Function and Bioinformatics

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