Statistical significance of protein structure prediction by threading

Statistical significance of protein structure prediction by threading.

In this study, we estimate the statistical significance of structure prediction by threading. We introduce a single parameter epsilon that serves as a universal measure determining the probability that the best alignment is indeed a native-like analog. Parameter epsilon takes into account both length and composition of the query sequence and the number of decoys in threading simulation. It can ...

Structure Prediction by Protein Threading

The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on “the inverse protein folding problem” laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet p...

Protein structure prediction by threading : force field philosophy ,

Protein fold recognition by prediction-based threading.

In fold recognition by threading one takes the amino acid sequence of a protein and evaluates how well it fits into one of the known three-dimensional (3D) protein structures. The quality of sequence-structure fit is typically evaluated using inter-residue potentials of mean force or other statistical parameters. Here, we present an alternative approach to evaluating sequence-structure fitness....

Mapping Monomeric Threading to Protein-Protein Structure Prediction

The key step of template-based protein-protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mappin...