Evolutionary profiles improve protein–protein interaction prediction from sequence

Evolutionary profiles from the QR factorization of multiple sequence alignments.

We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identifi...

Application of multiple sequence alignment profiles to improve protein secondary structure prediction.

The effect of training a neural network secondary structure prediction algorithm with different types of multiple sequence alignment profiles derived from the same sequences, is shown to provide a range of accuracy from 70.5% to 76.4%. The best accuracy of 76.4% (standard deviation 8.4%), is 3.1% (Q(3)) and 4.4% (SOV2) better than the PHD algorithm run on the same set of 406 sequence non-redund...

Human protein-protein interaction prediction by a novel sequence-based co-evolution method: co-evolutionary divergence

MOTIVATION Protein-protein interaction (PPI) plays an important role in understanding gene functions, and many computational PPI prediction methods have been proposed in recent years. Despite the extensive efforts, PPI prediction still has much room to improve. Sequence-based co-evolution methods include the substitution rate method and the mirror tree method, which compare sequence substitutio...

Prediction of DNA-binding sites in proteins using evolutionary profiles

Combining sequence and structural profiles for protein solvent accessibility prediction.

Solvent accessibility is an important structural feature for a protein. We propose a new method for solvent accessibility prediction that uses known structure and sequence information more efficiently. We first estimate the relative solvent accessibility of the query protein using fuzzy mean operator from the solvent accessibilities of known structure fragments that have similar sequences to th...