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Scientific Reports, ISSN 2045-2322, 12/2018, Volume 8, Issue 1, pp. 13694 - 14
Difficulty in sampling large and complex conformational spaces remains a key limitation in fragment-based de novo prediction of protein structure. Our previous... 
REFINEMENT | ROSETTA | ENERGY | NOVO STRUCTURE PREDICTION | SEQUENCES | MULTIDISCIPLINARY SCIENCES | ALGORITHM | SCORING FUNCTIONS | OPTIMIZATION | DIVERSITY | PROBABILISTIC SEARCH | Problem solving | Exploration | Sampling | Protein structure
Journal Article
Molecular Biology and Evolution, ISSN 0737-4038, 09/2015, Volume 32, Issue 9, p. 2456
  Recent developments in the analysis of amino acid covariation are leading to breakthroughs in protein structure prediction, protein design, and prediction of... 
Proteins | Molecules | Phylogenetics | Evolution | Amino acids
Journal Article
Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, 08/2000, Volume 40, Issue 3, pp. 389 - 408
All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms.... 
structure validation | explicit hydrogens | reversed leucines | van der Waals analysis | side‐chain rotamer library | all‐atom contact analysis | Side-chain rotamer library | Structure validation | All-atom contact analysis | Van der Waals analysis | Explicit hydrogens | Reversed leucines
Journal Article
Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, 04/2016, Volume 84, Issue 4, pp. 411 - 426
Journal Article
Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, 02/2003, Volume 50, Issue 3, pp. 437 - 450
Geometrical validation around the Cα is described, with a new Cβ measure and updated Ramachandran plot. Deviation of the observed Cβ atom from ideal position... 
Ramachandran plot | bond‐angle deviations | 3D protein structure | strained conformations | all‐atom contact analysis | γ‐turn | Bond-angle deviations | γ-turn | All-atom contact analysis | Strained conformations
Journal Article
Biomolecules, ISSN 2218-273X, 10/2019, Volume 9, Issue 10, p. 612
Our previous work with fragment-assembly methods has demonstrated specific deficiencies in conformational sampling behaviour that, when addressed through... 
Journal Article
Molecular Biology and Evolution, ISSN 0737-4038, 12/2011, Volume 28, Issue 12, p. 3331
Evolution of new cellular functions can be achieved both by changes in protein coding sequences and by alteration of expression patterns. Variation of... 
Proteins | Correlation analysis | Genomes | Gene expression | Binding sites
Journal Article
Journal Article
by Anderson, Beverley H and Kasher, Paul R and Mayer, Josephine and Szynkiewicz, Marcin and Jenkinson, Emma M and Bhaskar, Sanjeev S and Urquhart, Jill E and Daly, Sarah B and Dickerson, Jonathan E and O'Sullivan, James and Leibundgut, Elisabeth Oppliger and Muter, Joanne and Abdel-Salem, Ghada M. H and Babul-Hirji, Riyana and Baxter, Peter and Berger, Anea and Bonafé, Luisa and Brunstom-Hernandez, Janice E and Buckard, Johannes A and Chitayat, David and Chong, Wui K and Cordelli, Duccio M and Ferreira, Patrick and Fluss, Joel and Forrest, Ewan H and Franzoni, Emilio and Garone, Caterina and Hammans, Simon R and Houge, Gunnar and Hughes, Imelda and Jacquemont, Sebastien and Jeannet, Pierre-Yves and Jefferson, Rosalind J and Kumar, Ram and Kutschke, Georg and Lundberg, Staffan and Lourenço, Charles M and Mehta, Ramesh and Naidu, Sakkubai and Nischal, Ken K and Nunes, Luís and Ounap, Katrin and Philippart, Michel and Prabhakar, Prab and Risen, Sarah R and Schiffmann, Raphael and Soh, Calvin and Stephenson, John B. P and Stewart, Helen and Stone, Jon and Tolmie, John L and van der Knaap, Marjo S and Vieira, Jose P and Vilain, Catheline N and Wakeling, Emma L and Wermenbol, Vanessa and Whitney, Anea and Lovell, Simon C and Meyer, Stefan and Livingston, John H and Baerlocher, Gabriela M and Black, Graeme C. M and Rice, Gillian I and Crow, Yanick J and Medicinska fakulteten and Medicinska och farmaceutiska vetenskapsområdet and Institutionen för kvinnors och barns hälsa and Uppsala universitet
Nature genetics, ISSN 1061-4036, 2012, Volume 44, Issue 3, pp. 338 - 342
Journal Article
Molecular Biology and Evolution, ISSN 0737-4038, 11/2010, Volume 27, Issue 11, p. 2567
Protein-protein interactions effectively mediate molecular function. They are the result of specific interactions between protein interfaces and are maintained... 
Proteins | Amino acids | Molecular biology | Evolution & development
Journal Article
Nature Genetics, ISSN 1061-4036, 11/2012, Volume 44, Issue 11, pp. 1243 - 1248
Journal Article