The evolutionary trajectory of a protein through sequence space is constrained by its
function. Collections of sequence homologs record the outcomes of millions of evolutionary …

Motivation: The accurate prediction of residue–residue contacts, critical for maintaining the
native fold of a protein, remains an open problem in the field of structural bioinformatics …

We show that amino acid covariation in proteins, extracted from the evolutionary sequence
record, can be used to fold transmembrane proteins. We use this technique to predict …

The most accurate characterizations of the structure of proteins are provided by structural
biology experiments. However, because of the high cost and labor-intensive nature of the …

Predicting protein structure from primary sequence is one of the ultimate challenges in
computational biology. Given the large amount of available sequence data, the analysis of …

Motivation: Protein residue–residue contacts continue to play a larger and larger role in
protein tertiary structure modeling and evaluation. Yet, while the importance of contact …

Protein contact map prediction is useful for protein folding rate prediction, model selection
and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map …

The advent of high accuracy residue-residue intra-protein contact prediction methods
enabled a significant boost in the quality of de novo structure predictions. Here, we …

Knowing the quality of a protein structure model is important for its appropriate usage. We
developed a model evaluation method to assess the absolute quality of a single protein …

Motivation Residue–residue contacts are of great value for protein structure prediction, since
contact information, especially from those long-range residue pairs, can significantly reduce …