Prediction of protein subcellular localization based on primary sequence data

Download
2003
Özarar, Mert
Subcellular localization is crucial for determining the functions of proteins. A system called prediction of protein subcellular localization (P2SL) that predicts the subcellular localization of proteins in eukaryotic organisms based on the amino acid content of primary sequences using amino acid order is designed. The approach for prediction is to nd the most frequent motifs for each protein in a given class based on clustering via self organizing maps and then to use these most frequent motifs as features for classication by the help of multi layer perceptrons. This approach allows a classication independent of the length of the sequence. In addition to these, the use of a new encoding scheme is described for the amino acids that conserves biological function based on point of accepted mutations (PAM) substitution matrix. The statistical test results of the system is presented on a four class problem. P2SL achieves slightly higher prediction accuracy than the similar studies.

Suggestions

Prediction of protein subcellular localization based on primary sequence data
Ozarar, M; Atalay, Mehmet Volkan; Atalay, Rengül (2004-04-30)
Subcellular localization is crucial for determining the functions of proteins. A system called prediction of protein subcellular localization (P2SL) that predicts the subcellular localization of proteins in eukaryotic organisms based on the amino acid content of primary sequences using amino acid order is designed. The approach for prediction is to find the most frequent motifs for each protein in a given class based on clustering via self organizing maps and then to use these most frequent motifs as featur...
Prediction of protein subcellular localization using global protein sequence feature
Bozkurt, Burçin; Atalay, Mehmet Volkan; Department of Computer Engineering (2003)
The problem of identifying genes in eukaryotic genomic sequences by computational methods has attracted considerable research attention in recent years. Many early approaches to the problem focused on prediction of individual functional elements and compositional properties of coding and non coding deoxyribonucleic acid (DNA) in entire eukaryotic gene structures. More recently, a number of approaches has been developed which integrate multiple types of information including structure, function and genetic p...
FTIR spectroscopic characterization of protein structure in aqueous and non-aqueous media
Haris, PI; Severcan, Feride (1999-09-15)
With increasing use of proteins in many different applications, ranging from phramaceuticals to biosensors and biomaterials, there has emerged a need for protein structural characterisation in diverse environments. In many cases it is not sufficient to just have the three-dimensional structure of a protein in H2O or in the crystalline state. Often information on the structural properties of a protein is required in the presence of organic solvents, detergent micelles, phospholipid membranes and so on. Fouri...
Multi-view subcellular localization prediction of human proteins
Özsarı, Gökhan; Atalay, M. Volkan.; Department of Computer Engineering (2019)
Determining the subcellular localization of proteins is crucial for Understanding the functions of proteins, drug targeting, systems biology, and proteomics research. Experimental validation of subcellular localization is an expensive and challenging process. There exist several computational methods for automated prediction of protein subcellular localization; however, there is still room for better performance. Here, we propose a multi-view SVM-based approach that provides predictions for human proteins. ...
Predicting Protein-Protein Interactions from the Molecular to the Proteome Level
Keskin, Ozlem; Tunçbağ, Nurcan; Gursoy, Attila (2016-04-27)
Identification of protein protein interactions (PPIs) is at the center of molecular biology considering the unquestionable role of proteins in cells. Combinatorial interactions result in a repertoire of multiple functions; hence, knowledge of PPI and binding regions naturally serve to functional proteomics and drug discovery. Given experimental limitations to find all interactions in a proteome, computational prediction/modeling of protein interactions is a prerequisite to proceed on the way to complete int...
Citation Formats
M. Özarar, “Prediction of protein subcellular localization based on primary sequence data,” M.S. - Master of Science, Middle East Technical University, 2003.