Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?

By Ilya N. Shindyalov, N. Kolchanov, Christopher Sander. 1994

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Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, methodology): “This suggests that residue correlations could provide information about amino acid residues that are close in structure [4,5,6,7,8,9,10,11].”
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 ”
Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners (2014, neutral): “ssian distribution is parametrized by a mean vector = ( i) i=1;:::;N and a covariance matrix = ( ij) i;j=1;:::;N . Its probability density is P(xj;) = (2 ˇ) N 2 j j 1 2 exp 1 2 (x )T 1(x ) ; (4) j jbeing the determinant of , and it turns out that the Q Qblock e kl (a;b) = 1 (k 1)Q+a;(l 1)Q+b (5) (”
Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction (2015, background): “The idea has already been introduced in the early 1990s [8 – 11], however, until recently, the accuracy of the predicted contacts was not sufficient to significantly improve structure prediction methods.”
Correlated mutations contain information about protein-protein interaction. (1997, background): “Several groups have studied correlated mutations: technical differences between different approaches have led to con¯icting conclusions about the nature and intensity of this phenomena (Altschuh et al., 1987, 1988; Go È bel et al., 1994; Neher, 1994; Shindyalov et al., 1994; Taylor & Hatrick, 1994).”
Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction (2018, background): “In multiple sequence alignments (MSAs) of related proteins, this eﬀect leads to correlations between columns of residues in contact among most protein family members [19, 20, 42, 51].”
Assessing the accuracy of contact predictions in CASP13 (2019, background): “18,19 At the time, the low accuracy of contact predictions had limited success in assisting protein structure modeling at CASP 11,12,20 but was successfully employed in specific applications, such as folding small proteins, 21 improving statistical pair potentials, 22 selecting models in fold…”