Function prediction from networks of local evolutionary similarity in protein structure

Combining evolutionary and structural information for local protein structure prediction.

We study the effects of various factors in representing and combining evolutionary and structural information for local protein structural prediction based on fragment selection. We prepare databases of fragments from a set of non-redundant protein domains. For each fragment, evolutionary information is derived from homologous sequences and represented as estimated effective counts and frequenc...

Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs.

A new method to analyze the similarity between multiply aligned protein motifs (blocks) was developed. It identifies sets of consistently aligned blocks. These are found to be protein regions of similar function and structure that appear in different contexts. For example, the Rossmann fold ligand-binding region is found similar to TIM barrel and methylase regions, various protein families are ...

Accurate Prediction of Docked Protein Structure Similarity

One of the major challenges for protein-protein docking methods is to accurately discriminate nativelike structures. The protein docking community agrees on the existence of a relationship between various favorable intermolecular interactions (e.g. Van der Waals, electrostatic, desolvation forces, etc.) and the similarity of a conformation to its native structure. Different docking algorithms o...

Prediction of protein function from structure: insights from methods for the detection of local structural similarities.

Hierarchical Multilabel Protein Function Prediction Using Local Neural Networks

Protein function predictions are usually treated as classification problems where each function is regarded as a class label. However, different from conventional classification problems, they have some specificities that make the classification task more complex. First, the problem classes (protein functions) are usually hierarchically structured, with superclasses and subclasses. Second, prot...