Prediction of protein secondary structure content for the twilight zone sequences.
نویسندگان
چکیده
Secondary protein structure carries information about local structural arrangements, which include three major conformations: alpha-helices, beta-strands, and coils. Significant majority of successful methods for prediction of the secondary structure is based on multiple sequence alignment. However, multiple alignment fails to provide accurate results when a sequence comes from the twilight zone, that is, it is characterized by low (<30%) homology. To this end, we propose a novel method for prediction of secondary structure content through comprehensive sequence representation, called PSSC-core. The method uses a multiple linear regression model and introduces a comprehensive feature-based sequence representation to predict amount of helices and strands for sequences from the twilight zone. The PSSC-core method was tested and compared with two other state-of-the-art prediction methods on a set of 2187 twilight zone sequences. The results indicate that our method provides better predictions for both helix and strand content. The PSSC-core is shown to provide statistically significantly better results when compared with the competing methods, reducing the prediction error by 5-7% for helix and 7-9% for strand content predictions. The proposed feature-based sequence representation uses a comprehensive set of physicochemical properties that are custom-designed for each of the helix and strand content predictions. It includes composition and composition moment vectors, frequency of tetra-peptides associated with helical and strand conformations, various property-based groups like exchange groups, chemical groups of the side chains and hydrophobic group, auto-correlations based on hydrophobicity, side-chain masses, hydropathy, and conformational patterns for beta-sheets. The PSSC-core method provides an alternative for predicting the secondary structure content that can be used to validate and constrain results of other structure prediction methods. At the same time, it also provides useful insight into design of successful protein sequence representations that can be used in developing new methods related to prediction of different aspects of the secondary protein structure.
منابع مشابه
Prediction of protein structural class for the twilight zone sequences.
Structural class characterizes the overall folding type of a protein or its domain. This paper develops an accurate method for in silico prediction of structural classes from low homology (twilight zone) protein sequences. The proposed LLSC-PRED method applies linear logistic regression classifier and a custom-designed, feature-based sequence representation to provide predictions. The main adva...
متن کاملProtein Secondary Structure Prediction: a Literature Review with Focus on Machine Learning Approaches
DNA sequence, containing all genetic traits is not a functional entity. Instead, it transfers to protein sequences by transcription and translation processes. This protein sequence takes on a 3D structure later, which is a functional unit and can manage biological interactions using the information encoded in DNA. Every life process one can figure is undertaken by proteins with specific functio...
متن کاملSequence representation and prediction of protein secondary structure for structural motifs in twilight zone proteins.
Characterizing and classifying regularities in protein structure is an important element in uncovering the mechanisms that regulate protein structure, function and evolution. Recent research concentrates on analysis of structural motifs that can be used to describe larger, fold-sized structures based on homologous primary sequences. At the same time, accuracy of secondary protein structure pred...
متن کاملBeyond the Twilight Zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information.
The prediction of 1D structural properties of proteins is an important step toward the prediction of protein structure and function, not only in the ab initio case but also when homology information to known structures is available. Despite this the vast majority of 1D predictors do not incorporate homology information into the prediction process. We develop a novel structural alignment method,...
متن کاملAn Extensive Report on Cellular Automata Based Artificial Immune System for Strengthening Automated Protein Prediction
Artificial Immune System (AIS-MACA) a novel computational intelligence technique is can be used for strengthening the automated protein prediction system with more adaptability and incorporating more parallelism to the system. Most of the existing approaches are sequential which will classify the input into four major classes and these are designed for similar sequences. AIS-MACA is designed to...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Proteins
دوره 69 3 شماره
صفحات -
تاریخ انتشار 2007