Ab initio folding of proteins using restraints derived from evolutionary information

By Angel R. Ortiz, Andrzej Kolinski, Piotr Rotkiewicz, B. Ilkowski, Jeffrey Skolnick. 1999

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Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, background): “Previous work combined a small number of evolutionarily inferred residue contacts with other, structural, sources of information to successfully predict the structure of some smaller proteins, [16,17,18,19].”
Protein sectors: evolutionary units of three-dimensional structure (2009, background): “Indeed, several reports have proposed approaches for the calculation of residue covariance, but often with the goal of identifying the pattern of contacts in the three dimensional structure (Gobel et al., 1994; Hamilton et al., 2004; Larson et al., 2000; Neher, 1994; Olmea and Valencia, 1997; Ortiz ”
Statistical potentials for fold assessment (2002, unknown): “The fold has to be assessed almost invariably for all of the models predicted by ab initio methods (Jones 1997; Ortiz et al. 1999; Xia et al. 2000; Bonneau and Baker 2001; Pillardy et al. 2001) and threading of sequences into structures (Bowie et al.”
Co-evolving residues in membrane proteins (2007, methodology): “The significance of each prediction was evaluated using a 2-test.”
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison (2002, background): “The availability of large number of structures and sequences is fueling encouraging developments in ab initio protein structure prediction (Orengo et al. 1999; Ortiz et al. 1999; Simons et al. 1999) and related techniques.”
3D Protein Structure Predicted from Sequence (2011, unknown): “Previous work combined a small number of evolutionary inferred residue contacts with other, structural, sources of information to successfully predict the structure of some smaller proteins, [14,15,16,17].”
EVA: evaluation of protein structure prediction servers (2003, background): “... calculated accuracy divided by the random accuracy (13); (iii) distance distribution of the predicted contacts—the weighted harmonic average difference between the predicted contact distance distribution and the all-pairs distance distribution (14); and (iv) delta evaluation—the percentage of co”
Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners (2002, background): “Knowing the correct positions of residue contacts in proteins has proven to be extremely useful in determining the three-dimensional structure of a given protein, as demonstrated in the CASP3 and CASP4 experiments (see http://predictioncenter.llnl.gov/ and Ortiz et al. (1999); Lesk et al. (2001)).”
From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction (2012, unknown): “The direct use of correlations for discovering structural constraints such as residue-residue contacts in a protein fold has, unfortunately, remained of limited accuracy [5,6,9,11,13,16].”