TAILIEUCHUNG - Feature selection for indexing protein structures

Protein is composed of amino acids which are, in turn, made up of mostly carbon, hydrogen, oxygen, nitrogen. A protein structure consists of thousands of coordinates of its atoms. Building structure index tables (often organized by suffix trees or arrays) of proteins is an important phase for quickly searching or classifying protein structures. | JOURNAL OF SCIENCE OF HNUE Natural Sci. 2011 Vol. 56 No. 7 pp. 32-43 FEATURE SELECTION FOR INDEXING PROTEIN STRUCTURES Luong Van Hieu Hanoi Vocational College for Electro-Mechanics Pham Tho Hoan Hanoi National University of Education E-mail hoanpt@ Abstract. Protein is composed of amino acids which are in turn made up of mostly carbon hydrogen oxygen nitrogen. A protein structure consists of thousands of coordinates of its atoms. Building structure index tables often organized by suffix trees or arrays of proteins is an important phase for quickly searching or classifying protein structures. Most previous studies use only structural features to build the index tables therefore searching and classifying performances based on these index tables are not good enough. In this paper we propose two methods of feature selection to create index tables that contain not only structural features but also sequantial features. Experiments on a protein classification dataset called SCOP showed that our proposed feature selection methods considerably improve the searching and classifying performances when compared with previous feature selection methods. Keywords Protein structure indexing feature selection. 1. Introduction The goal of Life Sciences is to understand the function of biological molecules such as the protein DNA RNA. While biology technologies can now easily deter- mine the sequence or 3D structure of biological molecules it is difficult to discover the functions of the biological molecules. However the structures of the sequence proteins especially 3D structures may be important information to predict their functions based on the previously known functions of other proteins with similar structures. In general the problem of structural search and comparison can be solved through two main phases firstly extracting informative feature vectors of 3D structures secondly representing and organizing these feature vectors by some ap- propriate data structures .

• Giáo dục học
• Protein structure
• Feature selection
• A protein structure consists
• Previous feature selection methods
• Protein classification dataset
• BMC Bioinformatics
• Fragment based protein structure prediction
• Protein secondary structure
• Significantly model quality
• Protein’s possible
• Protein structure prediction
• Bioinformatics tool
• Secondary structure
• Solvent accessibility
• Contact map
• Tertiary structure
• Protein model quality assessment
• Secondary structure elements
• Inter SSE contacts
• Protein tertiary structure
• Principles of biochemistry
• Lecture Principles of biochemistry
• Biological systems
• Biochemical compounds
• Protein folding
• Protein 3 D structure
• Protein structure ranking
• Poor quality protein structural
• Linear combination
• Ab initio fragment based protein structure prediction
• Protein structural class
• Fragment based protein
• Molecular dynamics simulations
• Domain of unknown function
• Protein family
• YARHG domain
• Sequence analysis
• BMC Plant Biology
• Gene duplication
• Homology modelling
• Manganese stabilizing protein
• Oxygen evolving complex
• Parallel evolution
• Scientific reports
• scientific research
• biochemistry
• PA TM RING proteins have an N terminal protease associated domain
• a structure found in numerous proteases and implicated in protein binding
• and C terminal RING finger and PEST domains
• Homologous proteins include GRAIL (gene related to anergy in leukocytes)
• which controls T cell anergy
• and AtRMR1 (receptor homology region transmembrane domain RING H2 motif protein)
• a plant protein storage vacuole sorting receptor
• Deep sequencing
• Next generation sequencing
• High throughput
• Protein evolution
• Protein design
• Protein biophysics
• Structural biology
• Protein contacts
• Structure reconstruction
• Secondary structures
• De novo structure prediction
• Deuterium exchange
• Isotopic fine structure
• Fourier transform ion cyclotron resonance
• Mass spectrometry
• Protein analysis
• Decoy database
• Comparative modeling
• Three dimensional structure
• X ray crystallography alone
• Statistical potential
• Pair wise interaction
• Protein decoy set
• Distance cutoff
• Model selection
• Raptor X
• Protein structure methods
• Template based modeling
• Homology modeling
• Random forest
• Machine learning
• Protein sequence
• Whey protein
• Structural analysis
• Accelerate yoghurt fermentation
• Facilitate yoghurt structure
• Yoghurt structure
• Protein Synthesis
• Protein Degradation
• Proteins Consumed
• Bacterial Protein
• Conformational Changes
• Evolutionary coupling analysis
• Computational protein design
• Protein protein interaction networks
• Protein complex
• Overlapping node
• Seed extension paradigm
• Node betweenness
• Evolutionary information
• Inverse Protein Folding
• Coevolution analysis
• Coevolving residues
• Co occurring residues
• Covariation of residues
• Protein function
• Protein annotation
• Protein sequence analysis
• Fast protein contact prediction
• 2D prediction
• Open source software
• BMC Genomics
• Graph clustering algorithms
• Functional properties