Protein Structure Mining Using A Structural Alphabet

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Mining protein loops using a structural alphabet and

Mining protein loops using a structural alphabet and statistical exceptionality because they are highly variable in terms of sequence and structure, are it is the first time that pattern

Unravelling the Architecture of Membrane Proteins with

crystallography and NMR spectroscopy on these proteins. Structural determination of IMPs can be problematic due to difficulties in obtaining sufficient amounts of sample. A further contributing factor is that IMPs are generally much more likely to become inactive while handling or waiting for crystallization [17].

BMC Bioinformatics BioMed Central - Springer

protein structure [9]. The HP model is based on the obser-vation that the hydrophobic force is the main force deter-mining the unique native conformation (and hence the functional state) of small globular proteins [9,10]. In the HP model, the primary amino acid sequence of a protein (which can be represented as a string over a


using its deep-learning tools to target rare, single-gene disorders for drug development. MINING GENOMIC DATA When it comes to deep learning, not just any data will do. The method often requires massive, well-annotated data sets. Imaging data provide a natural fit, but so, too, do genomic data. One biotech firm that is using such data is

Protein quality assessment - PLU

protein structure predictions. Curr. Opin, Struct, Biol, 1996 Simons, K.T. et al. Improved recognition of native like protein structures using a combination of sequence dependent and sequence independent features of proteins. 1999. Rykunov, D.&Fiser,A. New statistical potential for quality assessment of protein

Introduction to Bioinformatics Sequence analysis

If protein structure, even secondary structure, can be accurately predicted from the now abundantly available gene and protein sequences, such sequences become immensely more valuable for the understanding of drug design, the genetic basis of disease, the role of protein structure in its enzymatic, structural, and signal


protein s primary structure i.e., sequence only. For this purpose, the datasets are extracted form Protein Data Bank(PDB), a curated protein family database, are used as training datasets. In these conducted experiments, the performance of the classifier is compared to other known data mining approaches / sequence comparison methods.

ProteinClassificationin aMachineLearningFramework

The 3-dimensional (3D) structure of a protein, called the secondary structure, is evolved by folding the chain of its own amino acids, called protein folding , in such a Figure 2.1: The Central Dogma of molecular biology.

Graphlet Kernels for Prediction of Functional Residues in

the structural neighborhoods of residues under consideration and measured in terms of local pat‐ terns of inter‐residue connectivity. We start by modeling a protein structure as a protein contact graph, where each amino acid is represented by a vertex in the graph and two vertices are con‐

The glycan alphabet is not universal: a hypothesis

Jan 15, 2020 An additional factor contributes to the diversity in the primary structure of glycans viz., microheterogeneity (Johannessen et al. 2012), a feature not seen in DNA or proteins (Table 1). These structural variations demand the use of multiple analytical was not certified by peer review) is the author/funder.

Identification of Local Conformational Similarity in

determined protein structure, mining the structural databases enables the identification of protein structures/sub-structures similar to the given structure [13 18]. Proteins are not rigid macromolecules and they exhibit certain degree of flexibility to allow structural variations critical for functional mechanisms [19].

Capturing the Right Signals: String Kernels for Protein

Identify the local structural regions of the protein. Contact-map prediction Identify the pairs of residues that will be in contact in the protein s 3D structure. Fold recognition Determine whether or not the protein s tertiary structure will adopt a shape that is similar to that of a known 3D structure. New-fold prediction

2015 OPEN ACCESS pharmaceuticals - MDPI

Nov 16, 2015 2.1.2. Structure From the limited number of members identified thus far, thionins have relatively conserved amino acid sequences compared to other plant defense peptides (Figure 1A). They also share a conserved β1-α1-α2-β2-coil secondary structural motif, which forms a gamma (Г) fold, a special turn consists of

Computer System Gene Discovery for Promoter Structure Analysis

(3) Comparing predicted structural or functional regions with similar regions on related genes (using information accumulated in available databases); (4) Providing functional annotation of the gene sequence. Our approach is based on Data Mining methods for construction and description of specific oligonucleotide promoter patterns [9].

Assignment of Protein Sequence to Functional Family Using

Protein classification prediction is an important problem in molecular biology, and one that has attracted a lot of attention. This paper describes an approach to data-driven discovery of sequence motif-based models using neural network classifier based on Dempster-Shafer Theory for assigning protein sequences to functional families.

Mining RNA Tertiary Motifs with Structure Graphs

protein, RNA has four levels of structural organization: primary, secondary, tertiary, and quaternary. Primary structure is the linear sequence of nucleotides, Secondary structure is the collection of pairs of bases in 3D structure, tertiary structure is the overall shape of an RNA molecule, and quaternary structure is the

Model-based classification for subcellular localization

alphabet size for the Markov Chains using the knowledge about structural properties of amino acids, learning classifiers from different regions of the protein sequences. I have empirically evaluated several meta-learning schemes, such as stacking, arbitration, grading and construction of the decision tree of base classifiers.

Protein is incompressible - University of Waikato

The structure of protein Proteins make up much of the structure of the cell, and also act as molecular machines to perform the work of transporting molecules, replicating DNA, transmitting signals, expelling waste, and so on. Proteins are sequences drawn from a 20 symbol alphabet of amino acids, listed in Table 2. Alphabet structure

Statistical Machine Learning Methods for Bioinformatics IV

Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins. 2002 J. Cheng, A. Randall, M. Sweredoski, and P. Baldi. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Research. 2005.

A Constraint Logic Programming Approach to 3D Structure

Keywords: Protein structure, constraint logic programming, parallelism Reference to this paper should be made as follows: A. Dal Palu`, E. Pontelli, J. He and Y. Lu. A Constraint Logic Programming Approach to 3D Structure Determination of Large Protein Complexes , Int. J. Data Mining and Bioinfor-matics, Vol. x, No. x, xxx.

Learning Classifiers for Assigning Protein Sequences to Gene

Proteins are the principal catalytic agents, structural elements, signal transmitters, transport-ers and molecular machines in cells. Experimental determination of protein structure and function significantly lags behind the rate of growth of protein sequence databases. This situa-tion is likely to continue for the foreseeable future.

iPBAvizu: a PyMOL plugin for an efficient 3D protein

A structural alphabet is a library of protein fragments able to approximate every part of protein structures (for a re-view [20]). These libraries yielded prototypes that are rep-resentative of local folds found in proteins. The structural alphabet allows the translation of three-dimensional pro-tein structures into a series of letters.

Prediction of protein secondary structure by mining

Prediction of protein secondary structure by mining structural fragment database Haitao Chenga, Taner Z. Sena, Andrzej Kloczkowskia, Dimitris Margaritisb, Robert L. Jernigana,* aDepartment of Biochemistry, Biophysics and Molecular Biology, L.H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University,


residues ignoring any other protein in the pdb file. ´By using AMIGOS we can do angle mining of (structural alphabet) letters.

Recent developments in the Inorganic Crystal Structure

materials science (Fig. 1). Pure structure information is combined with information on physical chemical properties and measurement methods. This means that the data can be used more universally. Last but not least, as a result of discussions about data mining and the application of semantic tools, article- and structure-related keywords (not


classification of genetic data (biosequences, protein structure data, microarray gene expression, etc.). SVM is a structural risk minimization-based method for creating binary classification functions from a set of labeled training data. SVM requires that each data instance is represented as a vector of real numbers in feature space. Hence, if

Mining Quantitative Association Rules in Protein Sequences

structural genes [1]. The proteins are sequences made up of 20 types of amino acids. Each amino acid is represented by a single letter alphabet, see Table 1. Each protein adopts a unique 3-dimensional structure, which is decided com-pletely by its amino-acid sequence. A slight change in the sequence might com-

Feature Selection using Relative Reduct hybridized with

four structural classes such as all α, all β, all α + β and all α / β are considered as decision attribute d as shown in Table 1. The protein feature vector constructed using amino acids composition that represents a simple sequence that is widely used in prediction of various structural aspects. When

A Machine Text-Inspired Machine Learning Approach for

accuracy, we combine domain insights from structural biology with machine learning techniques proven for the analogous task of topic segmentation in text mining. 1.1 G Protein Coupled Receptors G Protein Coupled Receptors (GPCRs) are transmembrane proteins that serve as sen-sors to the external environment.

Use of a structural alphabet to find compatible folds for

the most widely used structural alphabet in terms of applications.25,26 The description of protein struc-tures in terms of PBs may be applied to protein structure analysis, comparison, and mining.27 31 To-date there is no method that can directly score the compatibility of an amino acid sequence with known structures using sequence structure

Graphlet Kernels for Prediction of Functional Residues in

in Protein Structures VLADIMIR VACIC,1 LILIA M. IAKOUCHEVA,2 STEFANO LONARDI,1 AND PREDRAG RADIVOJAC3 ABSTRACT We introduce a novel graph-based kernel method for annotating functional residues in protein structures. A structure is first modeled as a protein contact graph, where nodes correspond to residues and edges connect spatially

Prediction of bacterial E3 ubiquitin ligase effectors using

protein sequences we have developed a machine learning approach, the SVM-based Identification and Evaluation of Virulence Effector Ubiquitin ligases (SIEVE-Ub). We extend the string kernel approach used previously to sequence classification by introducing reduced amino acid (RED) alphabet encoding for protein sequences. Results.

A Relational Extension to the Notion of Motifs: An

we will focus our attention on the application in structural molecular biology, that is finding repeated substructures in 3D protein structures, using as rela-tions the distances between the α-carbons in the protein structure. Notice that this data differs from that used in Feng et al. (2005) and Parida and Zhou (2005)

Sub2Vec: Feature Learning for Subgraphs -

such as social networks, protein-protein interaction networks, the World Wide Web, and so on. Analysis of such networks include classification [1], detecting communities [2, 3], and so on. Many of these tasks can be solved using machine learning algorithms. Unfortunately, since most machine learning algorithms require data to be represented

SA-conf: a tool to identify variable regions in a set of

SA-conf: a tool to identify variable regions in a set of related protein using a join analysis of their sequence and local structure defined by a structural alphabet Leslie Regad1,2, Jean-Baptiste Chéron1,2, Caroline Senac1,2, Triki Dhoha1,2, Delphine Flatters1,2, Anne-Claude Camproux1,2 1 INSERM, UMRS 973, MTi, Paris, France

GOR Method for Protein Structure Prediction using Cluster

units are referred to as secondary structure. Important factors in protein secondary structure are the angles and hydrogen bond patterns between the backbone atoms. A common pattern in protein forms the secondary structure. Secondary structure is further divided into three parts: alpha-helix, beta-sheet, and loop. 3.

Introduction to Bioinformatics

Protein folding though thermodynamically reversible in-vitro, is expected to depend on complex cellular processes E.g. chaperone molecules Prediction of protein folded structure and function from sequence is hard Biological function is not known for roughly half of the genes in every genome that has been sequenced Lack of technology

Detecting Protein Candidate Fragments Using a Structural

Citation: Shen Y, Picord G, Guyon F, Tuffery P (2013) Detecting Protein Candidate Fragments Using a Structural Alphabet Profile Comparison Approach. PLoS ONE 8(11): e80493. doi:10.1371/journal

Scalable Sequential Pattern Mining for Biological Sequences

to sequential pattern mining to biosequences. Our experi-ments show that this solution does not scale because of the following features for biosequences. Small alphabet. Biosequences have a very small alpha-bet, i.e., 4 for DNA sequences and 20 for protein sequences, and many short patterns occur in most sequences. In con-