Fold Recognition Using Sequence Fingerprints of Protein Local Substructures
نویسندگان
چکیده
A protein local substructure (descriptor) is a set of several short non-overlapping fragments of the polypeptide chain. Each substructure describes local environment of a particular residue and includes only those segments of the main chain that are located in the proximity of that residue. Similar descriptors from the representative set of proteins were analyzed to reveal links between the substructures and the sequences of their segments. Using the detected sequence-based fingerprints, specific geometrical conformations are assigned to new sequences. The ability of the approach to recognize correct SCOP folds was tested on 273 sequences from the 49 most popular folds. Good predictions were obtained in 85% of cases. No performance drop was observed with decreasing sequence similarity between target sequences and sequences from the training set of proteins.
منابع مشابه
Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins.
An all-against-all protein structure comparison using the Combinatorial Extension (CE) algorithm applied to a representative set of PDB structures revealed a gallery of common substructures in proteins (http://cl.sdsc.edu/ce.html). These substructures represent commonly identified folds, domains, or components thereof. Most of the subsequences forming these similar substructures have no signifi...
متن کاملFast screening of protein surfaces using geometric invariant fingerprints.
We develop a rapid and efficient method for the comparison of protein local surface similarities using geometric invariants (fingerprints). By combining fast fingerprint comparison with explicit alignment, we successfully screen the entire Protein Data Bank for proteins that possess local surface similarities. Our method is independent of sequence and fold similarities, and has potential applic...
متن کاملHow the Sequence of a Gene Specifies Structural Symmetry in Proteins
Internal symmetry is commonly observed in the majority of fundamental protein folds. Meanwhile, sufficient evidence suggests that nascent polypeptide chains of proteins have the potential to start the co-translational folding process and this process allows mRNA to contain additional information on protein structure. In this paper, we study the relationship between gene sequences and protein st...
متن کاملIdentification of an Ideal-like Fingerprint for a Protein Fold using Overlapped Conserved Residues based Approach
Design of an efficient fingerprint that detects homologous proteins at distant sequence identity has been a great challenge. This paper proposes a strategy to extract an ideal-like fingerprint with high specificity and sensitivity from a group of sequences related to a fold. The approach is devised based on the assumptions that the critical residues for a protein fold may be conserved in three ...
متن کاملImproving taxonomy-based protein fold recognition by using global and local features.
Fold recognition from amino acid sequences plays an important role in identifying protein structures and functions. The taxonomy-based method, which classifies a query protein into one of the known folds, has been shown very promising for protein fold recognition. However, extracting a set of highly discriminative features from amino acid sequences remains a challenging problem. To address this...
متن کامل